According to the Statute, approved by the Government of the Republic of Lithuania in 1999, the students of the academy were divided into three major categories: cadets, officer course students and the other students. Besides, the institution was responsible for military training of higher educational institution students.

One of the basic requirements for the countries seeking membership to NATO was to radically reform their leadership policy, i.e. to train officer in accordance with NATO standards. Taking it into account, the Ministry of National Defence by the end of 1999, provided the means for the modernization of the Military academy of Lithuania, and for the development of officers training requirements.

On June 21, the Museum of the Academy was founded. The museum was responsible for the collection, accumulation, and preservation of the material relevant to the history of the Academy and other military training institutions of Lithuania.

Cadets proved their abilities at peacekeeping exercises „Cooperative best effort 99“ in Canada.

The school was proud of 83 graduates and their diplomas of bachelor, 75 of them completed the mechanized riflemen study programme, and 8 - interior service programme.

The men choir „Kariűnas“ (Warrior) represented Academy at Baltic States’ Student Song Festival “Gaudeamus XII“ in Vilnius.

The Baltic States joint defence college BALTDEFCOL opened its doors in Tartu, Estonia.