APEIR's organizational structure consists of country representatives, country coordinator focal points, and the APEIR coordinating office to run the organization in day-to-day basis. APEIR’s working principle is based on mutual trust and a partnership concept. Below is the organizational structure of APEIR.

1. A regional partnership steering committee (SC): The SC consists of 2 representatives from each of the countries involved in the Partnership - Cambodia, China, Indonesia, Laos, Thailand and Vietnam - as well as representatives from several donor organizations including IDRC. The SC is responsible for providing overall guidance, coordination and supervision.
2. A small supporting regional coordinating office (CO): The CO is based at Indonesia One Health University (Indohun), and is led by an Asian coordinator. The CO is responsible for managing the day-to-day organizational matters of the Partnership, which include: (i) supporting all regional activities planned by the Partnership; (ii) sharing information relevant to national and regional coordination; (iii) organizing and planning SC and other related meetings; and (iv) assisting country focal persons to link research findings to regional and international policy.
3. Country Coordinator: Each country assigns a country coordinator who is responsible for coordinating Partnership activities. This person is affiliated with one of the Partner institutions, and serves as the main point of contact for communicating and coordinating national activities of the Partnership, and bringing all necessary partners within the country together to develop the network. The country coordinator's role is to coordinates national activities decided by the Steering Committee, and to work closely with the Steering Committee and the Coordinating Office to ensure that the country’s participation in the various Partnership research activities runs smoothly.
4. Group of partners for collaborative research programs: Research groups were formed by researchers from the Partnership member countries to jointly develop research proposals, and implement research activities in each country with the same framework and methodologies. Findings from the studies are shared within the Partnership and with other donors. One lead institution from each research group is responsible for coordinating overall research and overall reporting to IDRC and the Partnership Steering Committee.