After graduation, Khachaturov was appointed commander of a platoon in the artillery regiment of the motor rifle division of the Far Eastern Military District of the Soviet Army.

Khachaturov served as chief of staff of the missile forces and artillery of the 5th Guards Motor Rifle Division of the 40th Army in Afghanistan from 1987 to February 1989.

After serving in Afghanistan, Khachaturov was appointed commander of the separate artillery brigade of a tank army of the Belarusian Military District in October 1989.

[5] Khachaturov also held the post of commander of rapid deployment units and the Deputy Chief of the General Staff of the Armed Forces of the Republic of Armenia.

[6] On July 26, 2018, Khachaturov was arrested and charged with "overthrowing the constitutional order" in connection with his actions as commander of the Yerevan garrison during the events of March 1-2, 2008, when opposition protests led by Levon Ter-Petrosyan were suppressed by police and military forces, resulting in several deaths (Ter-Petrosyan had accused the authorities of rigging the results of the presidential elections held in February of that year).

[7][8] Khachaturov was tried alongside ex-president Robert Kocharyan, ex-defense minister Seyran Ohanyan (who was Chief of the General Staff in March 2008), and former secretary of the Security Council Armen Gevorgyan.