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:

Study Group on “the U.S.-Japan Alliance in the era of Japan as a Proactive Contributor to Peace” (Project Leader: KAMIYA Matake, Director and Superior Research Feollow, 2015-2016)

Study Group on “Grand Design of the U.S.-Japan Alliance at a New Stage”（Project Leader: KAMIYA Matake, Director and Superior Research Fellow, 2013-2014

Study Group on “Prospects and Challenges for the Formation of International Public Goods in the Era of ‘Smart Power’: Deepening and Enlarging of the Concept of ‘an Alliance’” (Project Leader: KAMIYA Matake, Councilor and Senior Research Fellow, 2011～2012)

Study Group on “the Japan-U.S. Alliance and Japanese Foreign Policy in the Era of ‘Smart Power’” (Project Leader: KAMIYA Matake, Councilor and Senior Research Fellow, 2010)

"East Asia Forum (EAF)" aims at enhancing understanding and cooperation among industry-government-academia in ASEAN+3 nations.

"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.

"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.

"Japan-U.S. Joint Research Program on Counter Piracy" aimed to explore how the Japan-U.S. relations could contribute in addressing piracy, which in recent years has become a source of threat to the international community.

Report "The Global Maritime Security and the Japan-U.S. Alliance"

"Study Group on Japan's National Strategy" aimed to play the role of a bridgehead for strengthening strategic way of thinking in Japan. The members of the Study Group consisted of scholars, politicians and government officials.

"Building on the TCOG: Enhancing Trilateral Policy Coordination Among the United States, Japan, and the Republic of Korea" (2004-2005) is a research project in collaboration with the Institute for Foreign Policy Analysis (IFPA) in the U.S. and Yonsei University's Graduate School of International Studies (GSIS) in Korea, exploring the prospects for expanding the TCOG process as a Key U.S.-South Korea and U.S.-Japan Alliance management tool.

Project Overview
Article about the TCOG project by James L. Schoff, Senior Staff Member, Institute for Foreign Policy Analysis and Principal Investigator for 'Building on the TCOG' Project
First Interim Report on the TCOG

"Japan in Asia: What Should We Do?" (2002-2004) is a research project, examining "Asia as Political System (first year)" and "Asia as Economic System (second year)" by holding dialogues with intellectuals in Asian countries, and convening an international symposium on "Japan in Asia and its role."

The First Term (2002): "Japan in Asia: What Should We Do?"-Asia as a Political System-
The Second Term(2003):"Japan in Asia: Asia as Economic System"

"Redefining the U.S.-Japan Alliance: Toward Building a Security Community" (2001-2005) is a research project, co-sponsored with the Sigur Center for Asian Studies, The George Washington University, examining the U.S.-Japan Alliance as a public good for peace and stability in the Asia Pacific region from both theoretical and policy perspectives.

"Symposium on Building the Financial System of the 21st Century: An Agenda for Japan and the United States" (2000-2002), co-sponsored with the Harvard Law School, aims to further understanding between Japan and the USA on financial matters.

"Domestic Sources and Constraints of Japan's International Contributions" (1998-2007) was a research project co-sponsored with the Brookings Institution examining influences of domestic political structures and norms on Japanese international contributions. It has held workshops in both Tokyo and Washington, and includes the changing international situation after the September 11 terrorist attacks within its purview. A book on the study group’s findings was published in March 2007.

"Maritime Nation Seminar" (1998-2001) was convened as a forum for discussion to analyze Japan's identity and its grand strategy as a nation in the 21st Century.

The First Term (1998): Japan's Identity: Neither the West Nor the East

The Second Term (1999): Japan's Grand Strategy For the 21st Century: From an Insular Nation to a Maritime Nation

The Third Term (2000): The Vision of The maritime Nation of Japan: The World Order and the Regional Order

The Fourth Term (2001): The Maritime Nation of Japan: Civilization and its Strategy

"The Grand Strategy Study Group" (1997) aimed to deepen interest and theoretical understanding of nation state strategies especially amongst young researchers.

"The Japan Council on Nuclear Energy, Environment & Security" (1995-2002) was initiated to examine the possibility of nuclear disarmament and the perspective of nuclear energy globally but with special focus on a fast growing Asia.

"The International Study Group on Preventive Diplomacy" (1996-1998) was established to study the role of preventive diplomacy in the post-Cold War world. The recommendations of this Group led to the establishment of the Japan Center for Preventive Diplomacy (JCPD) in 1999 as an affiliated organization to JFIR. Thereafter, in February 2002, JCPD obtained independent legal status as a non-profit organization and changed its name to the Japan Center for Conflict Prevention (JCCP).

"The 21st Century Seminar" (1994-1997) examined fundamental issues in the post Cold War era with dialogues in Tokyo, Kuala Lumpur and Sinaia, Romania.
The Japan Forum on International Relations (JFIR)