The Antonov An-12 plane, which was heading to a factory in Irkutsk, caused a fire at the military unit, but there were no casualties on the ground.
Six crew members and three others on board were killed.
The authorities have given no explanation for the crash, but Russia has a poor air-safety record.
Accidents are relatively frequent and planes are often poorly maintained, according to safety experts.
A Russian cargo plane has crashed into warehouses at a military facility in Siberia, killing all nine people on board, officials have said.