Collaboration with the United Nations and its agencies to strengthen effective civil-military relations is a key focus of the Centre's work.

• UN Office for the Coordination of Humanitarian Affairs (UN OCHA). Through its focus area of Disaster Management, Humanitarian Assistance and Reconstruction, the Centre works with UN OCHA's Civil-Military Coordination cell in Geneva, and with the regional office in Bangkok on common areas of interest.  In 2008, the Centre co-hosted with UN OCHA the 3^rd Asia Pacific Conference on Military Assistance to Disaster Relief Operations, and continues to work with OCHA to develop guidelines in this area. The Centre will also contribute to UN OCHA's civil-military coordination training courses in the Asia Pacific region, and will work closely with UN OCHA to enhance awareness of the protection of civilians in complex emergencies.
• UN Department of Peacekeeping Operations (DPKO). Through its focus areas of peace & stabilisation operations, and governance & the rule of law, the Centre works with DPKO to enhance civil-military relations. Typical areas of developing interest include: integrated mission planning, the development of civil-military relations guidelines, civil-military best practice, protection of civilians, security sector reform, and police-military collaboration.
• UN Department of Political Affairs (DPA).  Through its focus area of conflict prevention the Centre is able to assist DPA in areas of civil-military relations. In late 2008 the Centre's Executive Director led a UN assessment team to the United Nations Mission in Nepal (UNMIN) to advise the Special Representative of the Secretary General on the next phase of UNMIN's mission (refer Centre News). The Centre's assistance was acknowledged in the Secretary-General's report to the Security Council.
• UN Institute for Training and Research (UNITAR).  Through its training, education & research mandate, the Centre will seek to establish a relevant linkage with UNITAR on civil-military issues to assist UNITAR in fulfilling its mission to deliver innovative training and conduct research on knowledge systems to develop the capacity of beneficiaries.
• UN Peacebuilding Commission. As it matures, the Centre will seek to establish linkages with the Peacebuilding Commission on mutual civil-military areas of interest. The Peacebuilding Commission is an advisory body of the United Nations that supports peace efforts in countries emerging from conflict, and is a key addition to the capacity of the International Community in the broad peace agenda.
• UN Agencies. The Centre will look to partner with specific UN programmes and agencies on relevant areas of civil-military relations where such collaboration is seen to be mutually beneficial. Such agencies may include the United Nations Development Programme (particularly the Bureau for Conflict Prevention and Recovery), the United Nations High Commissioner for Refugees (UNHCR), the World Food Programme (WFP), the United Nations Population Fund (UNFPA),  the United Nations Development Fund for Women (UNIFEM), and the Office of the High Commissioner for Human Rights (OHCHR).