A military official was quoted as saying that the explosion occurred at about 8:30 am local time at a submarine repair dock in Jinhae, South Gyeongsang province, which serves as home for the South Korean navy.
The accident happened while a midget submarine was being repaired, but the exact cause of the explosion was yet to be confirmed.
Among the two wounded, one is in critical condition.
The missing person was thrown into the water from the shock of the explosion.
All of those killed, wounded and missing were commissioned or uncommissioned officers, the military official was quoted as saying.