"We can confirm there was an explosion. Emergency responders are on the scene," Lieutenant Greg Raelson told AFP.
At least six employees suffered injuries and were taken to local hospitals, the Navy said in a series of tweets.
Local media said the explosion took place during maintenance work on a vessel at the Naval Weapons Station Earle in Middletown, New Jersey.
But the Navy said ammunition and ordnance operations at the facility were "not affected" by the blast.
About 1,500 people work at the naval station, which is used as a weapons depot and for ship repairs.