The SECI Agenda Committee represented the decision-making body and motivating force behind the initiative and consisted of high-ranking government officials from each participating and supporting state. It dealt with identifying common areas of concern relating to the economy and environment of the region, as well as proposing short lists of priorities on the basis of which projects will be planned and implemented. The Agenda Committee convened four to five times a year. Until September 2000 SECI Agenda Committee Meetings were held at the United Nations Economic Commission for Europe (UN ECE) in Geneva.

Later on, SECI Agenda Committee meetings were held prior to the with the Business Advisory Council to SECI meetings, which were held in the SECI countries. The idea to hold meetings in different countries stemmed from the desire to strengthen the relationship and enhance the information flow between these core SECI bodies and to promote the active role which the SECI Participating States play within the initiative, as well as promulgate SECI's work in the region.

With the advent of the Stability Pact for South East Europe and in order to avoid duplication of efforts and overlapping, the SECI Agenda Committee meetings were held back to back with the meetings of the Regional National Coordinators of the Stability Pact and upon necessity. With the change of the regional cooperation mechanisms that took place in South East Europe in the last few years, the National Coordinators of the SECI Countries remained an integrative part of the SECI collaborators network and are regularly consulted and informed on the ongoing activities of the Initiative.