The helicopter crashed and caught fire during a test flight after repairs at the base in the port city of Pohang, the ministry said in a statement.
"Five of the six crew members on board were killed and the remaining one has been taken to hospital due to injury," it said.
The ministry said an investigation into the cause would be launched but did not specify whether all victims were soldiers.
The helicopter was a domestically made model known as the MUH-1 or Marineon, Yonhap news agency said.