U.S. intelligence involvement with World War II Japanese war criminals
At the end of the Second World War, U.S. intelligence agencies, most of which were predecessors of the current organizations, protected some war crimes suspects in return for information of intelligence value.
OSS, however, had a much more limited role in the Pacific, primarily in China. General of the Army Douglas MacArthur essentially banned the OSS from his Southwest Pacific Area (SWPA), while OSS simply was less relevant to the naval and "island hopping" operations in Fleet Admiral Chester Nimitz's Pacific Ocean Area (POA; Nimitz was referred to as CINCPAC [Pacific] /CINCPOA) theater. Since there was no postwar alliance to be preserved for US intelligence, there were few reasons to keep matters classified due to the sensitivities of a key ally. While the US did work with Australia and New Zealand, MacArthur had essentially subordinated their commands. 
The number and types of Japanese who formed relationships with U.S. intelligence differ from their Nazi counterparts. The Japanese were fewer in number than the Germans who were directly to collect HUMINT from the Soviets or take part in stay-behind networks after invasion. Some of the Japanese were imprisoned for investigation, or actually served prison time for war crimes, perhaps being released early. Far more of the Japanese were later at a much higher level of authority than were the Germans.
U.S. intelligence conflict in postwar Japan
MacArthur's distaste for the OSS continued into an equal reluctance to allow the CIA to operate in the Occupation, until he was relieved of duty. Until his relief, MacArthur used his own intelligence organization, G-2, headed by Major General Charles Willoughby (a confidante of MacArthur). Japanese ex-officers and nationalists, immediately after the war, created an informal network intended to preserve, as far as possible, the Imperial system and eventually to reestablish the military. Subsequently, the CIA referred to these as "underground" groups, although not in the sense that they were resistance organizations.
Most US contacts with the underground groups were combat rather than intelligence specialists. With the exception of Arisue Seizo and a few key others, most of the links established by U.S. authorities to the Japanese “underground” groups, as the CIA called the Japanese networks, were to highranking officers with operational and combat experience. Another significant intelligence specialist, with an extensive network of contacts among officers, was Lieutenant General Torashiro Kawabe. Kawabe joined with Arisue in providing the services of former Japanese Army personnel to occupation authorities, particularly G-2. Kawabe’s last headquarters assignment gave him informal authority over many groups and individuals within the army. His network was made up primarily of former high-ranking army general staff members and their subordinates. These individuals were in networks of subordinate organizations, called kikan, that would carry out actual operations. 
In one important case, that of Shiro Ishii, the intelligence cooperation was not for shaping the political destiny of postwar Japan or for obtaining future intelligence, but as a trade of immunity for technical data.
Since the relationships often were established after a convicted or investigated Japanese left prison, the working relationships started later than did those with Germans. Some of the Japanese eventually reached Cabinet or Prime Ministerial level. In at least one case, that of Kodama Yoshio with Kishi Nobusuke, the close working relationship grew when they were cellmates.
Japanese who worked with US intelligence
A variety of relationships existed, first with G-2 and then with the CIA. Characteristic of the G-2 relationships was a significant amount of delegation of both planning and execution to Japanese, since SCAP did not itself have the manpower for detailed monitoring, nor would it work with CIA in the theater or in the US.
After his rehabilitation in 1950, Masanobu Tsuji received U.S. funding through the G-2’s Historical Branch under Willoughby. Through Arisue, G-2 recruited and employed some 200 former Japanese officers to assist historian Gordon Prange’s work on the history of MacArthur’s Pacific campaign. A central figure in this effort was Colonel Takushiro Hattori . One of the most important members of the Hattori kikan, known in some CIA documents as “Willoughby’s Stable,” was Hattori’s close friend Masanobu Tsuji.
The key individual in the "undergrounds" was Lieutenant General Seizo Arisue , chief of the intelligence department at Imperial General Headquarters at the end of the war. Shortly before the end of the war, Arisue began collecting intelligence documents to use as a bargaining chip with the Occupation.
SCAP sentiment toward Arisue was mixed, and officers outside G-2 considered indicting Arisue as a Class A war criminal. Willoughby, however, had met and liked Lieutenant General Torashiro Kawabe who had been head of intelligence for the Kwangtung Army, military attaché to Berlin, deputy chief of staff for Imperial GHQ, and the leader of the surrender delegation to Manila.
Willoughby asked Arisue, in September 1945, to set up a domestic intelligence network to warn of a potential Communist coup. Ironically, Willoughby was unaware that Arisue and some of his associates, at various times, considered right-wing coups against the Japanese government.
Hattori, a staff colonel, had served as a senior operations staff officer in the Kwantung Army during the Nomonhan Incident. Shortly afterwards, Hattori, became Chief of the Army General Staff Operations Branch, making him one of the principal planners of the successful Japanese Army offensives of 1941–42. He does not appear to have been under investigation for war crimes, but he had significant involvement with SCAP G-2 after the war. Hattori believed, along with his friend Tsuji, that the rearmament of Japan could not be achieved “through democratic methods,” and advocated a revival of the disbanded army, in which he would be Chief of Staff.
According to an AP article, the plot was developed after the U.S. postwar occupation of Japan ended in April 1952, by which time the US was no longer funding Hattori. Two CIA documents said the plot reportedly had the support of 500,000 people in Japan, and that the group planned to use a contact who controlled a faction inside the National Safety Agency - a precursor to the Defense Ministry - to help launch the coup. The article reinforces the lack of cooperation and common policy between SCAP G-2 and the CIA.
"Since the beginning of July 1952, plans for a coup d'etat have been initiated among a group of ex-purgees including former military officers. The leader of the group is ex-Colonel Hattori Takushiro," said an Oct. 31, 1952, report, which claimed "this report is the first to mention a definite rightist plan involving violence." "The original plan of the group was to engineer a coup d'etat, including the assassination of Prime Minister Yoshida Shigeru on account of his hostile attitude toward depurgees and nationalists," the CIA document said. "The group is considering the possibility of some minor assassination attempt in lieu of a coup d'etat," the Oct. 31, 1952, document said.
Perhaps the most blatant violator the Lieutenant General Shiro Ishii, head of the Japanese biological warfare program based at Unit 731 in Pingfan, China. Ishii, who had presided over human experimentation perhaps on a greater extent than the Nazis, and waged biological warfare against the Chinese, was given protection by CIC in exchange for data.
Department of State records refer to Okinori Kaya , a Class A war criminal, and wartime Finance Minister.  Kaya had been the finance minister in Japan's wartime cabinet. Convicted as a war criminal, he was sentenced to life in prison. Paroled in 1955 and pardoned in 1957, he became one of Kishi's closest advisers and a key member of the LDP's internal security committee.
Kaya started to work for the CIA around the time of his election to the Diet in 1958. After his recruitment, he wanted to travel to the United States and meet Allen Dulles in person. Kaya came to visit Dulles at CIA headquarters in 1959, and asked the director to enter into a formal agreement to share intelligence with his internal security committee. "Everyone agreed that cooperation between CIA and the Japanese regarding countersubversion was most desirable and that the subject was one of major interest to CIA", say the minutes of their talk. Dulles regarded Kaya as his agent, and six months later he wrote him to say: "I am most interested in learning your views both in international affairs affecting relations between our countries and on the situation within Japan". 
Kaya's on-and-off relationship with the CIA reached a peak in 1968, when he was the leading political adviser to Prime Minister Eisaku Sato. Kaya was instrumental in a CIA action intended to swing the Okinawan election to the LDP, an action that failed. Okinawa was a key U.S. base, both for Vietnam operations and nuclear basing. Kaya played a key role in the CIA's covert actions aimed to swing the elections for the LDP, which narrowly failed. Okinawa itself returned to Japanese administration in 1972, but the American military remains there to this day.
In 1941, Kishi was a Cabinet member who co-signed the declaration of war against the United States. During the war, he had held portfolios for Commerce and Industry and later Munitions, and directed forced labor by Koreans and Chinese. In 1945, he was arrested as a suspected Class A war criminal, and spent three years, in Sugamo Prison, being investigated. Eventually, he was not charged.  His cellmate was Kodama Yoshio. His political rehabilitation led to his becoming Prime Minister in 1957.
While the Occupation originally had bold goals to restructure and democratize Japanese society, ambitions became more modest as the Cold War chilled. Kennan's containment doctrine was the priority of the Truman Administration. United States Secretary of Defense James Forrestal said that real security against communism required the "restoration of commerce, trade and business" worldwide. This meant putting "Japan, Germany and other affiliates of the Axis back to work."
Before the war, Kishi had been a friend of U.S. Ambassador Joseph C. Grew. Grew, along with journalists, diplomats and lawyers, all of whom had had prewar ties with the Japanese elite. They opposed the SCAP policies calling for the renunciation of military capability.
After the end of the Korean War, and economic repercussions for Japan, the Yoshida government fell. The U.S. Ambassador in 1954, not intelligence officials, urged the conservative parties to name Kishi as Prime Minister. Another official who had been purged after the war, Hatoyama Ichiro, was selected. Hatoyama was reluctant to rearm, and wanted peaceful relations with China and the Soviets. These positions infuriated John Foster Dulles, United States Secretary of State in the Eisenhower Administration, whose brother Allen was Director of Central Intelligence. The Eisenhower Administration's support of Kishi became more and more obvious, when he made a state visit in 1957, addressing Congress and played golf with Eisenhower,
While detailed documentation has not been declassified, if it esists, indicates that early in 1958, Shaller states that Eisenhower, making what he and his aides earlier called a "big bet," authorized the CIA to provide secret campaign funds to Kishi and other members of the Liberal Democratic Party. The Administration agreed to renegotiate the 1951 security treaty and end the Occupation. In return for the right to use Okinawa as a base for nuclear forces, the U.S. renegotiated the treaty. While the Kennedy administration continued the secret payments, Although the Kennedy administration in 1961 continued secret payments to the LDP and other parties, "it viewed trade expansion as a better way to stabilize Japan and bind it to the United States."
Kodama was Kishi's cellmate in Sugamo Prison, from which they were released in 1948, before other convicted criminals were executed.  In 1928, he founded a right-wing group, the Dokuritsu Seinen Sha (Independence Youth Society). It tried to assassinate both opposition leaders and Prime Minister Saito Makoto, for which Kodama was sentenced to 3.5 years of imprisonment.
By the 1930s, he had been rehabilitated by the Japanese and formed both an intelligence network in Manchuria and an extensive system for purchasing strategic materials, such as cobalt, copper, nickel and radium, sometimes bartering drugs for materials. Kodama called it "an organization with no thought of profit," but, by the end of the war, it was worth $175 million and the Japanese government made the former prisoner a rear admiral. . After the war, Kodama began to pour part of his fortune into the careers of Japan's most conservative politicians, and he became a key member of a CIA operation that helped bring them to power. He worked with American businessmen, OSS veterans, and ex-diplomats to pull off an audacious covert operation, bankrolled by the CIA, during the Korean War.. This operation obtained tungsten needed for U.S. munitions, for which the United States Department of Defense paid $10 million, with underwriting of $2.8 million from the CIA.
According to Weiner, the operation left Kodama in bad odor with the CIA's Toyko station. "He is a professional liar, gangster, charlatan, and outright thief", the station reported on 10 September 1953. "Kodama is completely incapable of intelligence operations, and has no interest in anything but the profits". The relationship was severed, and the CIA turned its attention to the care and feeding of up-and-coming Japanese politicians - including Kishi - who won seats in the Diet, Japan's parliament, in the first elections after the end of the American occupation."
Recently declassified CIA documents explain why one of the most notorious Japanese war criminals was never indicted or even held. Arisue recruited Colonel Masanobu Tsuji into clandestine U.S. service. Tsuji, claiming the authority of Imperial General Headquarters, ordered a wide range of atrocities including the Bataan Death March.
CIA documents released through the IWG explained the puzzlement of many Japanese, who wondered why Tsuji was never charged for crimes sometimes worse that led to the gallows for others. Even after his release, he remained a "person of interest", but was not found to be interrogated.
He avoided capture first by hiding in Southeast Asia, later sheltered by Chiang Kai-shek on mainland China, then secretly in Japan, including as a guest of Kodama. When the United States dropped its war crimes charges against him in 1950, he returned to the public scene, publishing two books about his wartime and postwar experiences that quickly became best sellers. 
Before his rehabilitation, he was involved in G-2 planning of covert activities to assist the Chinese Nationalists against the Peoples Republic of China.  Note that direct confrontation with China, even through Chiang Kai-shek as a proxy, was against Truman Administration policy, a conflict that led to MacArthur's (and Willoughby's) dismissal.
By 1950, when there were no charges outstanding against Tsuji, Arisue asked him to expand Japanese intelligence operations into Southeast Asia.  Many of the other officers would not work with Tsuji and lobbied successfully to have Arisue replace him with former Shanghai kenpeitai Chief Tomita Bunichi. 
Through Hattori, Tsuji became involved in planning one of Willoughby’s most ambitious operations, a Chinese Nationalist invasion of mainland China. In January 1951, G-2 began toying with the notion of encouraging Chang Kai-shek’s forces to invade south China and establish contact with Chinese anti-communist resistance forces. Willoughby’s subordinates approached Hattori and requested that he and Tsuji prepare the operational details of such a plan. Hattori, whom the CIA believed was a key figure in getting the war crimes charges against Tsuji dropped, now sought to put Tsuji’s military expertise to work for G-2. Planning proceeded through early March, with Tsuji taking the lead. From the CIA’s perspective, Willoughby put undue trust in both Hattori and Tsuji. Tsuji, who had himself become enmeshed in rearmament plans, purportedly stated in 1951 that it was necessary to “deceive the ally prior to the enemy.” The agency’s analysts also saw “a serious danger that American military personnel in G-2, GHQ will be taken in by [Hattori’s group].” In any event, the planning came to very little, as Willoughby learned in March 1951 that news of the preparations leaked to the Communist Chinese, and the idea was shelved. 
By 1952, Tsuji and Hattori decided that cooperation with the Americans was the best way to rapidly rearm Japan, a position unpopular with many other ex-officers. Backed by Kodama and others, they disagreed with Prime Minister Shigeru Yoshida ’s policy of exclusively relying on U.S. military protection instead of rebuilding Japan’s own army. ...In July 1952, Hattori hatched a plot to conduct a coup by murdering Yoshida and replacing him either with the more sympathetic Ichiro Hatoyama or Taketora Ogata . While Tsuji initially supported a coup, Tsuji convinced Hattori to hold off his coup d’etat as long as the conservatives (of the ironically named Liberal Party) were in power. In other words, SCAP's staunchest political ally in Japan was protected by one of Japan’s most well-known alleged war criminals. Nevertheless, the group did consider murdering other government figures to send a message to Yoshida . Hatoyama succeeded in deposing Yoshida in 1954, but it is unclear what role, if any, Hattori and Tsuji played in this. In 1952, Tsuji was elected to the Diet and began a flamboyant career in politics, until his mysterious disappearance in 1961 during travel in Southeast Asia.
- National Archives and Records Administration Interagency Working Group (IWG) (March 2002), Implementation of the Japanese Imperial Government Disclosure Act and the Japanese War Crimes Provisions of the Nazi War Crimes Disclosure Act: An Interim Report to Congress
- Petersen, Michael (2006), Chapter 8: The Intelligence that Wasn't: CIA Name Files, the U.S. Army, and Intelligence Gathering in Occupied Japan, Researching Japanese War Crimes Records, National Archives and Records Administration Interagency Working Group (IWG)
- Associated Press (1 March 2007), CIA Papers Reveal Japan Coup Plot
- Tim Weiner (2007), Chapter 12: We Ran It in a Different Way, Legacy of Ashes: The History of the CIA, Doubleday
- Schaller, Michael (July 1995), America's Favorite War Criminal: Kishi Nobusuke and the Transformation of U.S.-Japan Relations, Japan Policy Research Institute
- , Kodama Yoshio, World Encyclopedia of Organized Crime, Zane Publishing