At NSC ISSAR there are two Specialized academic councils in Agricultural science and Biological science. Activities of academic councils are governed by regulations of the Cabinet of Ministers of Ukraine and the Ministry of Education and Science of Ukraine, Regulations on Specialized Academic Council and the Order of Awarding of Academic Degrees and Awarding Academic Rank of Senior Scientist.

• Specialized Academic Council D 64.354.01 with the right to consider and conduct defense of thesis for Doctor (PhD) degree of Agricultural Sciences in the specialty 06.01.03 - agropedology and argophysics and 06.01.04 - Agrochemistry.
  Chairman – Prof.Baliuk S.A., Academician of the Academy of Agricultural Sciences, Doctor of Agricultural Sciences
  Vice-Chairman – Dr. Lisovy M.M., Doctor of Agricultural Sciences, Senior Researcher
  Secretary Assistant on Scientific Activity – Shymel V.V, PhD (Agricultural Sciences), Senior Researcher
• Specialized academic council K 64.354.02 with the right to consider and conduct defense of thesis for Doctor (PhD) degree in specialty 03.00.18 - Soil science.
  Chairman - Miroshnichenko M.M. Doctor of Biological Sciences, Senior Researcher
  Vice-Chairman – Tsapko Yu.L. Doctor of Biological Sciences, Senior Researcher
  Secretary Assistant on Scientific Activity – Makliuk O.I. PhD (Biological Sciences), Senior Researcher
  During the 1990-2016 by Specialized academic councils there were defended 35 doctoral and 250 PhD theses, during the last 5 years - 4 doctoral dissertations and 44 PhD theses.