World War II, submarine operations
In all ocean theaters of World War II, submarine warfare, as well as anti-submarine warfare, were critical parts of the war. German attacks on shipping to Great Britain nearly broke the flow of supplies to those islands, in what has been called the Battle of the Atlantic. U.S. submarines were even more effective against Japanese merchant shipping.
While all sides had individual spectacular kills against major warships, the Japanese overemphasized, perhaps from a warrior tradition, attacking warships rather than the logistics.
Submariners systematically avoided publicity, in order to encourage enemy overconfidence. Japan thought its defensive techniques sank 468 American subs; the true figure was only 42. (Ten others went down in accidents, the Atlantic Ocean, or as the result of friendly fire.) Submarines also rescued hundreds of downed fliers, most famously George H. W. Bush.
After its entry into the war, the U.S. reversed its opposition to unrestricted submarine warfare. The top German admirals, Erich Raeder and Karl Dönitz, were charged at the International Military Tribunal (Nuremberg), of violating international law through unrestricted submarine warfare; they were acquitted after proving British merchantmen were legitimate military targets under the rules in force at the time. Fleet Admiral Chester Nimitz, U.S. commander of Pacific forces, wrote to the tribunal that Doenitz had not done anything that U.S. submarines had not.
Submarine doctrine, command and control
Germany's submarine force, under Karl Doenitz, was extremely effective. Like the U.S. submarine service, it concentrated on merchant shippng. Doenitz had a doctrine of active centralized control of submarines, which, unknown to him, provided the Allies with a major source of signals intelligence, both from cryptanalysis of the Enigma machine, as well as direction finding.
Other nations gave their submarine captains much more autonomy, although a number of Japanese assets were diverted from combat, to supplying cut-off island garrisons.
In the Pacific, Allied submarines concentrated on destroying Japanese logistics, which was a center of gravity for an island nation. The importance of transport shipping was confirmed by the immense effect of German submarines on Britain, with the Battle of the Atlantic being as critical as the Battle of Britain.
Japan's torpedoes were superior to any others in the war, especially the Type 93 "Long Lance".
U.S. torpedoes, the standard issue Mark XIV torpedo and its Mark VI exploder were both defective, problems not corrected until September 1943.
While operations here were minor compared with those in the great oceans, there were individual events of note, rather than a long campaign,
Within hours of Pearl Harbor, Roosevelt ordered a new doctrine into effect: unrestricted submarine warfare against Japan. This meant sinking any warship, commercial vessel, or passenger ship in Axis controlled waters, without warning and without help to survivors.
Worst of all, before the war, an uninformed Customs officer had seized a copy of the Japanese merchant marine code (called the "maru code" in the USN), not knowing U.S. communications intelligence had broken it; Japan promptly changed it, and it was not recovered until 1943.
Thus it was not until 1944 the U.S. Navy learned to use its 150 submarines to maximum effect: effective shipboard radar installed, commanders seen to be lacking in aggression replaced, and faults in torpedoes fixed.
Japanese doctrine and equipment
For the Imperial Japanese Navy, however, submarines, as part of the Japanese warrior tradition of bushido, preferred to attack warships rather than transports. Faced with a convoy, an Allied submarine would try to sink the merchant vessels, while their Japanese counterparts would give first priority to the escorts. This was important in 1942, before Allied warship production came up to capacity. So, while the U.S. had an unusually long supply line between its west coast and frontline areas that was vulnerable to submarine attack, Japan's submarines were instead used for long range reconnaissance and to resupply strongholds which had been cut off, such as Truk and Rabaul.
Supply runs were a lesser drain on Allied resources. The problem of MacArthur's forces trapped in the Philippines led to diversion of boats to "guerrilla submarine" missions. As well, basing in Australia placed boats under Japanese aerial threat while en route to patrol areas, inhibiting effectiveness, and Nimitz relied on submarines for close surveillance of enemy bases. A small number of oversized submarines handled much of the resupply, submarines that were less agile than their sisters attacking escorted convoys.
Requirements of the Japanese Army to supply cut-off garrisons by submarine further reduced the effectiveness of Japanese anti-shipping warfare.  In addition, Japan honored its neutrality treaty with the Soviet Union, and ignored U.S. freighters shipping millions of tons of war supplies from San Francisco to Vladivostok.
A small number of Allied submarines--less than 2 percent of the fleet tonnage--strangled Japan by sinking its merchant fleet, intercepting many troop transports, and cutting off nearly all the oil imports that were essential to warfare. By early 1945 the oil tanks were dry.
U.S. submarines alone accounted for 56% of the Japanese merchantmen sunk; most of the rest were hit by planes at the end of the war, or were destroyed by mines. U.S. submariners also claimed 28% of Japanese warships destroyed. Furthermore they played important reconnaissance roles, as at the battles of the Philippine Sea and Leyte Gulf, when they gave accurate and timely warning of the approach of the Japanese fleet. Submarines operated from secure bases in Fremantle, Australia; Pearl Harbor; Trincomalee, Ceylon; and later Guam. These had to be protected by surface fleets and aircraft.
Fortunately, Japanese convoy protection was "shiftless beyond description" and convoys were poorly organized and defended compared to Allied ones, a product of flawed IJN doctrine and training, errors concealed by American faults as much as Japanese overconfidence. The number of U.S. submarines on patrol at any one time increased from 13 in 1942, to 18 in 1943, to 43 in late 1944. Half of their kills came in 1944, when over 200 subs were operating. By 1945, patrols had decreased because so few targets dared to move on the high seas. In all, Allied submarines destroyed 1,200 merchant ships. Most were small cargo carriers, but 124 were tankers bringing desperately needed oil from the East Indies. Another 320 were passenger ships and troop transports. At critical stages of the Guadalcanal, Saipan, and Leyte campaigns, thousands of Japanese troops were killed before they could be landed. Over 200 warships were sunk, ranging from many auxiliaries and destroyers to eight carriers and one battleship.
Underwater warfare was especially dangerous; of the 16,000 Americans who went out on patrol, 3,500 (22%) never returned, the highest casualty rate of any American force in World War II. The Japanese losses were even worse.
- "Japanese Torpedoes", Imperial Japanese Navy Page)
- Ladislas Farago, Broken Seal.
- Clay Blair, Silent Victory: The U. S. Submarine War Against Japan (1975) and Theodore Roscoe, United States Submarine Operations in World War II (1949).
- Carl Boyd, "The Japanese Submarine Force and the Legacy of Strategic and Operational Doctrine Developed Between the World Wars," in Larry Addington ed. Selected Papers from the Citadel Conference on War and Diplomacy: 1978 (1979) 27–40; Clark G. Reynolds, Command of the Sea: The History and Strategy of Maritime Empires (1974) 512.
- Larry Kimmett and Margaret Regis, U.S. Submarines in World War II
- Chihaya Masataka, in Pearl Harbor Papers, p.323. Chihaya went on to note, when IJN belatedly improved its ASW methods, the Sub Force responded by increasing Japanese loses.
- Roscoe, op. cit.