PROSEA operates as an autonomous, non profit international foundation registered in Indonesia. It based in Bogor, Indonesia and jointly managed and implemented by a network of institutions in five South East Asia countries (i.e. Indonesia, Malaysia, the Philippines, Thailand and Vietnam). The Netherlands was formerly involved from the beginning of its establishment as the Head Office as well as the Publication Office, and so was the Papua New Guinea as a country office, until year of 2003.
Significant changes have taken place in 2003, when the publication responsibility was transferred from the Publication Office in Wageningen, the Netherlands to the Network Office in Bogor, Indonesia. The Network Office has been developed into the PROSEA headquater, while the Wageningen University has been functioning as PROSEA Liason Office in Europe.