Pursuant to article XXIV of the Treaty, seven Special Commissions of the Amazon Region have been created for the study of specific problems and topics. The Commissions group the competent national institutions of each sector, thus making up an active subregional communication network.

- Health (Cesam) and Indigenous Affairs (Ceaia)
- Environment (Cemaa)
- Transport, Infrastructure and Communications (Ceticam) and Tourism (Cetura)
- Education (Ceeda) and Science and Technology (Cecta)

Special Commission of the Amazon Region on Health (CESAM)

In Article VIII of the Treaty, the Amazon countries decided to promote the coordination of health services in their Amazon territories and take the suitable measures to improve the health conditions of the region and to devise methods to fight and prevent epidemics.
CESAM was created in March 1988, as a sectorial coordination organ during the III Meeting of the Amazon Cooperation Council. CESAM has met four times, the last of which was in Lima in June 1995.

Special Commission of the Amazon Region on Indigenous Affairs (CEAIA)

CEAIA was created during the III Meeting of Ministers of Foreign Affairs of the ACT (March 1989) with the purpose of concretizing the regional interest for indigenous affairs. This Special Commission has met four times. The last meeting was held in Lima, in 1995.

Special Commission of the Amazon Region on the Environment (CEMAA)

This Commission was created during the III Meeting of Ministers of Foreign Affairs of the ACT (Quito, March 1989) to pursue the common objectives of environmental protection, as well as the rational use of the abundant and varied Amazon natural resources. The Commission has met five times; the last two Regular Meetings were held in Lima, in 1995 and in Santafé de Bogotá, in 1996.

Special Commission of the Amazon Region on Transport, Infrastructure and Communications (CETICAM)

The IV Meeting of the Amazon Cooperation Council (Santafé de Bogotá, May 1990) created the Special Commission of the Amazon Region on Transport (CETRAM). Subsequently, the IV Meeting of Ministers of Foreign Affairs of the ACT, held in Santa Cruz de la Sierra, Bolivia, in November 1991, enhanced its scope with the topics of communications and infrastructure, modifying its denomination to Special Commission of the Amazon Region on Transport, Infrastructure and Communications, (CETICAM).

In general terms, the programs and projects of this Special Commission are aimed at establishing strategies for the promotion of transport in its different modalities; preparing a general planning and projects on fluvial transport in the Amazonas river to develop trade and contributing to the well-being of the region; promoting the establishment of a land transportation system (road and railroad) and fostering the regional air transportation; facilitating telecommunications; carrying out pre-feasibility and feasibility studies or the priority inter-oceanic passageways and identifying intermode connection alternatives among the basins of the Amazonas, Orinoco and Plata rivers.

Special Commission of the Amazon Region on Tourism (CETURA)

CETURA was created during the IV Meeting of the Amazon Cooperation Council (Bogotá, May 1990) with the purpose of establishing suitable cooperation mechanisms for planning and creating the infrastructure necessary for tourist development of the Amazon Region.

This Commission has met three times; the last Regular Meeting was held in Lima in June 1995.

Special Commission of the Amazon Region on Education (CEEDA)

In the V Meeting of Ministers of Foreign Affairs of the Amazon Cooperation Treaty two decisions associated with education were made: the Special Commission of the Amazon Region on Education (CEEDA) was created as mechanism for evaluating experiences and coordinating the design of educational plans suited to the Amazon reality, in order to foster the education and training of human resources in the Amazon Region, as well as respect for the cultural identity of its peoples; and it was decided to common program to promote education and environmental awareness at school level and, to that end, they commissioned CEEDA to organize and call a regional seminar that shall propose orientations, content and scope of manuals to this end.

In 1997, the I Regular Meeting of this Special Commission and the "Regional Seminar on Preparation of Manuals for a Common Program for Promoting Environmental Education and Awareness at School Level" took place.

Special Commission of the Amazon Region on Science and Technology (CECTA)

CECTA was created during the III Meeting of the Amazon Cooperation Council (Brasilia, March 1988). It objectives include promoting and supervising the execution of regional projects and other activities undertaken by the Member Countries of the ACT in the fields of science and technology; and acting as mechanism to obtain financial resources from international sources and as coordinator of their use in regional programs. It has met five times; its last two Regular Meetings were held Lima in 1995 and in Iquitos in 1996.