Research and development institutions, cultural establishments and learned societies from outside the structure of the Academy may associate with the Academy on condition that their activities and objectives comply with the interests and aims of the Academy. Association of an institution or society with the Academy is executed in the form of a bilateral agreement, providing the aims of association as well as the reciprocal rights and obligations of the parties.
From 1989 onward, agreements of association have been signed with the following organisations:
Academic Library of Tallinn University
Institute of the Estonian Language
Estonian Literary Museum
Estonian National Museum
Estonian Crop Research Institute
Art Museum of Estonia
Agreements of association have been terminated with three partners: Institute of Zoology and Botany at Estonian Agricultural University, Institute of Ecology at Tallinn University, Institute for International and Social Studies at Tallinn University.