The videos were broadcast on the Enterprise's closed-circuit TV and included gay slurs and suggested scenes of women pretending to shower together. Other clips in the video show a man in drag and a mock rectal examination.
The Navy said it will investigate the videos it described as "clearly inappropriate."
In response to the videos, a Navy spokesman said the type of videos produced by Honors, "Were not acceptable then and are not acceptable in today's Navy," and that "U.S. Fleet Forces Command has initiated an investigation."
"Worst case is he could be taken to a court marshal," said Eugene Fidell of the National Institude of Military Justice. "It's a little bit of a challenge as to how you would charge this conduct, but they'll find something."
The Enterprise was deployed in the Middle East at the time the videos were made and is weeks from deploying again.
The Associated Press contributed to this report.