The helicopter, which was being test-flown after a repair, caught fire after it crashed to the ground from about 10 meters (33 feet) in the air, the ministry said.
One person survived the crash and was being treated at a nearby hospital, it said. The severity of the person's injury wasn't immediately known. The names of the pilots and passengers weren't immediately announced, AP reported.
The military plans to form a committee to investigate the cause of the crash.
Tuesday's crash was the second fatal accident involving South Korean military aircraft in recent months. Pohang is not far from where a South Korean F-15K fighter jet crashed into a mountain in April, killing both the pilot and co-pilot.