The incident happened Thursday night when a female officer claimed a 33-year-old lieutenant was trying to film inside the bathroom through a ventilation grate.
According to the female officer, who reported the incident, the suspect apologized and left the location when the officer approached.
"I am extremely disappointed in the alleged misconduct by a sailor temporarily embarked aboard our ship," Capt. Mike Wettlaufer, Stennis commanding officer, said in a statement.
"However, I am pleased a shipmate stepped up to stop unacceptable behavior and reported it. An NCIS investigation commenced immediately because our shipmate took action," he added.
The female officer later identified the suspect and the ship security took his electronic devices.
The suspect came aboard the aircraft carrier as part of the flight crew and he was taken out of the ship after the incident. His alleged misconduct also reported to his chain of command.
Cmdr. Jeanette Groeneveld, Naval Air Forces Pacific spokeswoman, said no more information will be released during the investigation that is expected to take a few weeks.
In November, other misconduct by Navy sailors was discovered in which a dozen of sailors allegedly viewed videos of their female colleagues in a submarine shower dressing area. The investigation about this incident aboard the ballistic-missile sub Wyoming, based in Kings Bay, Georgia is still going on.