In addition to the "Regular Research Programs" mentioned above, JFIR organizes multi-year "Special Research Programs" on an ad hoc basis to conduct research, exchanges, and recommendations on international and diplomatic issues that demand attention, with their outcomes announced to the public. The main "programs" which are under operation are as follows:
"Network of East Asian Think-tanks (NEAT)" aims at the creation of a network of think-tanks in ASEAN+3 nations, for research collaboration on the integration of the East Asia region.
"East Asia Forum (EAF)" aims at enhancing understanding and cooperation among industry-government-academia in ASEAN+3 nations.
"Russian Study Group" aims to study Japan's strategy toward Russia, particularly in relation to the Northern Territories issue.
"Chechnya Study Group" aims to raise understanding and awareness of the Chechnya issue in Japan. It invited to Japan an eleven member Chechnya delegation headed by Vice Premier Noukhaev in 1996.
- Prospects and Challenges for the Formation of International Public Goods in the Era of "Smart Power"(2011-2012)
- Japan-U.S. Joint Research Program on Counter Piracy (2009-2010)
- Study Group on Japan's National Strategy (2008-2009)
- Building on the TCOG: Enhancing Trilateral Policy Coordination Among the United States, Japan, and the Republic of Korea(2004-2005)
- Japan in Asia: What Should We Do? (2002-2004)
- Redefining the U.S.-Japan Alliance: Toward Building a Security Community (2001-2005)
- Symposium on Building the Financial System of the 21st Century: An Agenda for Japan and the United States (2000-2002)
- Domestic Sources and Constraints of Japan's International Contributions (1998-2007)
- Maritime Nation Seminar (1998-2001)
- The Grand Strategy Study Group (1997)
- The Japan Council on Nuclear Energy, Environment & Security (1995-2002)
- The International Study Group on Preventive Diplomacy (1996-1998)
- The 21st Century Seminar (1994-1997)