Research in maritime security started in 2004 following concerns over the security of ports and sea lanes in the Southeast Asian region. The Programme focuses on issues such as maritime terrorism, and piracy and armed robbery along the sea lanes. The Programme has produced policy papers such as the well received report Safety and Security in the Malacca and Singapore Straits.

The Contemporary Islam Programme (CIP) was formed to undertake independent studies on the role and perceptions of Islam in the context of politics and society in Southeast Asia. The Programme investigates Muslim attitudes in Southeast Asian studies on grassroots and elite perceptions of major issues pertaining to Islam's role in society attitudes towards Syariah, Jihad, etc.) The Programme also attempts to create institutional capacity by developing a core team of faculty members who undertake teaching as well as policy-relevant and scholarly research in various aspects of Muslim politics, jurisprudence, and state-society relations that is accessible to the wider public. Research by CIP members and associates include Shia Islam in Southeast Asia, political Islam in Malaysia and Indonesia, and the role of the Ulama in Malaysian society.

One of our earliest research efforts, the Indonesia Programme studies developments in the archipelago.This Programme focuses on national politics, political Islam, militant Islamic movements, civil-military relations, Singapore-Indonesia relations, and the political economy of the Riau. The diversity of research backgrounds in the Programme maximises the potential for cross disciplinary work on the problems of contemporary Indonesia. A significant part of the Indonesia Programme is its "Developments in Indonesia Public Lecture Series" which raised the Institute's profile in 1999 when it invited leaders of the reformasi movement - Abdurahman Wahid, Megawati Sukarnoputri and Amien Rais -to share their perspectives on post-Suharto developments in the country. Such initiatives also serve as a platform for networking between the Singapore policy community and the emerging political elite in Indonesia.

The China Programme in the Institute looks broadly at China's strategic thinking and behaviour. Its members provide a distinctive regional voice on the issue of the role of China as a rising power. The programme gives priority to research on the evolution of China's strategic thinking and behaviour, how these are influenced by domestic politics, by confidence building measures between China and regional states, and by regional institutions such as the ASEAN Regional Forum, 10+3 and the East Asian Summit; and how regional states' perceptions and behaviour toward China have been shaped as a result. The Programme also studies the military dimension of China's strategic thinking and behaviour and China's thinking and actions on issues such as anti-terrorism, maritime security and Taiwan. It also examines China and Japan-China relationships and their implications for the region and regional states.