During the Cold War, civil-military relations where essentially an internal matter; military cooperation focused on capacities. With the rise of the security sector reform (SSR) agenda, the UN and the donor community seek to actively shape the civil-military relations of countries emerging from conflict. The theme is heir to the impact of the Cold War`s decline on European integration, the development agenda, and UN peacekeeping operations. The agenda is contested by NGOs and the Non-Aligned Movement, concerned with the reduction of resources for development and increasing authority of the Security Council. In the case of Timor, the transitory administration of 1999 considered it had no role in support of the armed forces. After the 2006 crisis - in which army and police were involved in extreme politicization, human rights violations and serial desertion - the new peacekeeping operation was given an explicit mandate to support the review of the security sector. The study analyzes how the UN`s position in the field followed the evolution of the SSR agenda at headquarters.