Considering phenomenon of inter-institutional collaboration, the paper aims to investigate the issues of inter- institutional collaboration in Lithuanian public organizations. The paper is based on the study of collaboration aspects relevant to the project implemented by the Lithuanian Republic Ministry of Foreign Affairs. Based on theoretical discussion related to the success of project implementation and team work, two studies were conducted. Firstly, a sample comprised of seven project managers expressed the assumptions about decision-making process, obstacles of project implementation and measures for efficiency. Secondly, 65 responses were collected from project participants representing different public institutions. The results revealed that inter-institutional projects in public organizations are still characterized as following traditional and strictly hierarchic structure. The project leaders underestimate the potential of project group members and do not involve them into the decision-making process. The findings let us develop recommendations for managers and policy makers involved into inter-institutional projects.