In 2021, Lithuania faced the challenge of managing the crisis of new type of migration across the Belarusian border, which threatened the security of the country and its citizens. A broad set of inter-institutional collaboration strategies and methods were used among the public institutions to address this crisis. Such inter-institutional collaboration has been a multifaceted and complex process, involving both known and new good practices. The aim of this article is to provide insights into good collaborative practices between the Lithuanian national defence and internal affairs systems in managing the migrant crisis. Following the expert interview results, the study identified three good practices of inter-institutional collaboration: (i) the creation of a single dissemination channel for the crisis response services, which ensured that all actors were in the same information field; (ii) the delegation of representatives of the institutions to teams at strategic, operational and tactical levels; and (iii) inter-institutional information sharing ensured good situational awareness at an early stage of emergency management. Lessons learned from the collaboration between the institutions of the national defence and internal affairs systems can be applied to improve inter-institutional collaboration in other areas. The results of the research can be used to enhance the process of such collaboration in addressing current emergency management issues and serve as a basis for effective and smooth emergency preparedness and response where inter-institutional synergy is needed.