Participation in the process of PhD studies and training of highly qualified scientists is one of the primary tasks carried out by the NRC. In collaboration with other higher education institutions of Lithuania and those of other countries, the NRC implements the following five doctoral programmes: Ecology and Environmental Science (in collaboration with Vilnius University), Biology (in collaboration with Vytautas Magnus University, the State Research Institute Centre for Innovative Medicine, Geology (in collaboration with Vilnius University), Physical Geography (in collaboration with Vilnius University and Klaipėda University) and Zoology (in collaboration with Vilnius University). The number of dissertations defended at the Nature Research Centre in each of these fields during the 2018–2022 period is as follows: five dissertations in Biology, 22 dissertations in Ecology and Environmental Science, four dissertations in Geology, one dissertation in Physical Geography and one dissertation in Zoology. The number of students currently pursuing PhD studies in different fields of science is 50.
Besides active participation in the process of doctoral training, researchers of the Centre provide supervision of BSc and MSc degree theses in the fields of bioengineering, biology, botany, ecology and environmental research, genetics, geology, geography and zoology. Researchers also consult students during thesis/dissertation preparation, act as thesis/dissertation opponents or as members of the Dissertation Defence Board both in Lithuania and abroad.