Honors, who was then the carrier's executive officer, or second in command, starred in the short videos, shown with the logo XO Movie Night, The Virginian-Pilot in Norfolk, Va., reported today.
"Production of videos, like the ones produced four to five years ago on USS Enterprise and now being written about in the Virginian-Pilot, were not acceptable then and are still not acceptable in today's Navy," Navy spokesman Cmdr. Chris Sims said in a statement, according to CNN. "The Navy does not endorse or condone these kinds of actions."
The statement also said, "U.S. Fleet Forces Command has initiated an investigation into the circumstances surrounding the production of these videos; however, it would be inappropriate to comment any further on the specifics of the investigation."
According to the Virginian-Pilot, the videos were made with government equipment, and some were produced when the ship was actively deployed to help war efforts in Iraq and Afghanistan.
In the video posted on the newspaper's website, Honors says: "Over the years I've gotten several complaints about inappropriate material during these videos. Never to me personally but, gutlessly, through other channels."
He adds, "This evening, all of you bleeding hearts ...why don't just go ahead and hug yourselves for the next 20 minutes or so, because there's a really good chance you're gonna be offended. This evening we're gonna go through some racy topics."
The first topic, he says, always brings "easy laughs:" a string of clips edited together of him and others using "the F-bomb," which is repeatedly bleeped out on the newspaper's website. The video goes on to string together clips showing Honors and other sailors pretending to masturbate, set to a song called "Spank."
"Finally, let's get to my favorite topic," Honors says. "Something foreign to the gay kid over there -- chicks in the shower. This is certainly the most popular video of any of the XO Movie videos. It's also the one that's landed me with the most complaints."
The movies, written and produced by Honors and starring him, were shown about once a week on closed-circuit shipwide television, according to sailors interviewed by the Virginian-Pilot, which said they requested their names not be used for fear of reprisals.
A senior Navy official told NBC News that top officers became aware of the videos years ago and told Honors and others at the time to "knock it off."
The Enterprise is scheduled to deploy again within several weeks. But the Navy officials interviewed by NBC told the station that it now appears unlikely Honors will command the ship.
A Facebook fan page set up for supporters of the Enterprise was abuzz today with talk of the story, with many people commenting that they support Honors and appreciated his movies and humor.
One post read: "The XO movie night was one of the few things we looked forward to during deployment in '06. It is a shame that this distraction has been stirred up now years later."