[11] In March 1936, Choibalsan's Interior Ministry orchestrated the firing of his government and the removal Genden from the post of First Secretary of the Central Committee of the People's Revolutionary Party, due to his role in the deterioration of Mongol–Soviet relations.

[12] Just two months later the ministry amended its rules to include the detention high ranking politicians and public figures without first consulting any of its party or political superiors, effectively increasing its influence over the country.

Under the direction and guidance Choibalsan's Soviet handler Chopyak and other mentors from the NKVD, the ministry planned over the next three years to carry out the repressive purges on opponents of Stalin/Choibalsan, religious figures (mostly Buddhist Lamas) and enemies of the state.

When the purges ended, official blame was laid on the deputy minister of internal affairs Nasantogtoh, and his Soviet handler Kichikov.

[17][18][19] At the time of its original establishment, the Directorate of the Internal Troops was placed under the command of the Commissioner General, however, it was not fully clear what ministry has the ultimate control of it.