Role in transition
L. Paul Bremer remembers that al-Rubaie was one of the few who could bring humor to discussions, was a channel to Ayatollah Ali Sistani, and also could work compromise. Bremer called him an "honest messenger". In early August 2003, as frustrating discussions of budget were about to start between Bremer and the Iraqi Governing Council, he asked "Ambassador Bremer, Baghdad is abuzz with a press story that you are planning to marry several Iraqi women. So, Ambassador Bremer, the Council would like to know if this is true. 
Iraqi foreign policy
He spoke to the International Institute for Strategic Studies in December 2007, discussing issues with Iraq and its neighbors. In his opening statement, he observed that Iraq, Iran, and Saudi Arabia are neighbors, and one cannot change neighbors. They are bound by a common faith. "The region looks like a conflict between the industrialised West and our resource-rich region, with all three countries embroiled in that conflict. The region looks like a decade of simmering conflict, which has kept us apart, fighting amongst ourselves rather than cooperating for the good of the region, its people and the world. The choice is ours. Either a regional reconciliation, or a regional pettiness."
Acknowledging U.S. help, he said "the regional engagement of the Iraqi government with the four main neighbours – Iran, Turkey, Syria and Saudi Arabia – has been extremely successful over the last 12 months." He called for a regional security agreement. 
In July 2008, he that his government required a timetable for withdrawal before Iraq would sign an agreement about American forces in Iraq. "There should not be any permanent bases in Iraq unless these bases are under Iraqi control."
Current security activities
Iraq took responsibility for Camp Ashraf, a detention facility. He explained the government had decided to remove the Iranian terrorist group, Mojahedin-e Khalq (MEK, aka MKO, PMOI) from the country. In a situation ironically reminiscent of the U.S. government challenge on what to do with prisoners in Guantanamo Bay detention camp, he said "This is an indoctrinated and tightly disciplined organization of extremist zealots who have employed terrorism and at times even self-immolation to secure their aims. In normal everyda language we can say that they have been "brainwashed"...The Government of Iraq does not deal with the MEK as an organization. We deal with the residents as individuals." When asked by Iran-Interlink how governments could help deal with the MEK members, he said "These governments can agree to allow their citizens and others who have status in their country to return." 
- Coalition Provisional Authority (9 April 2004), Governing Councilmen Assume Posts as Minister of Interior and National Security Advisor
- L. Paul "Jerry" Bremer with Malcolm McDonnell (2006), My Year in Iraq: The Struggle to Build a Future of Hope, Simon & Schuster, ISBN 9780743273893, pp. 122-123
- Bremer, My Year in Iraq, pp. 295-296
- Mowaffak al-Rubae (9 December 2007). Iraq and the Neighbourhood. International Institute for Strategic Studies.
- Ernesto Londoño and Dan Eggen (9 July 2008), "Iraq Wants Withdrawal Timetable In U.S. Pact", Washington Post
- "Iraq's National Security Advisor Dr. Mowaffak al Rubaie on Camp Ashraf, Massoud Rajavi and 'Detoxifying' MEK Members", Reuters, April 6, 2009