Washington (CNN) -- The Navy captain who produced profanity- and slur-laden videos while second in charge of the USS Enterprise will be permanently relieved of his command of the ship, a top Navy commander said Tuesday.

The Navy will also investigate the role other senior officers played in the video scandal, Adm. John Harvey, commander of the U.S. Fleet Forces Command, said.

"While Capt. Honors' performance as commanding officer of USS Enterprise has been without incident, his profound lack of good judgment and professionalism while previously serving as executive officer on Enterprise calls into question his character and completely undermines his credibility to continue to serve effectively in command," Harvey said, reading from a prepared statement. He did not take questions.

Honors will be replaced by Capt. Dee Mewbourne, a former aircraft carrier commander who currently serves as chief of staff for the Navy Cyber Forces, Harvey said.

Honors has been reassigned to administrative duties with the Naval Air Force Atlantic command, Harvey said.

Excerpts from the videos and descriptions of their content were first published Saturday by The Virginian-Pilot newspaper in Norfolk, Virginia.

The videos on the paper's website, reviewed by CNN, feature a man identified by two Navy officials and The Virginian-Pilot as Honors, who at the time was the executive officer, or second in command, of the aircraft carrier. He recently took command of the carrier, winning one of the most coveted assignments in the U.S. Navy, which has only 11 aircraft carriers.

Navy spokesman Cmdr. Chris Sims said the videos, which were shown to the crew of the Enterprise while on deployment supporting the wars in Iraq and Afghanistan in 2006 and 2007, are "inappropriate."

Honors is shown cursing along with other members of his staff in an attempt to demonstrate humor, according to the videos.

There are also anti-gay slurs, simulated sex acts, and what appear to be two female sailors in a shower together.

The investigation was ordered Friday by Harvey, the four-star head of the Navy's Fleet Forces Command, after the videos were detailed in The Virginian-Pilot. The paper also posted a link to some of the material, but edited it so that expletives were censored and some identities of junior Navy crew were disguised.

"After personally reviewing the videos created while serving as executive officer, I have lost confidence in Capt. Honors' ability to lead effectively, and he is being held accountable for poor judgment and the inappropriate actions demonstrated in the videos that were created while he served as executive officer on Enterprise," Harvey said.

Harvey said that investigators will continue to examine the circumstances surrounding the production and distribution of the videos, which were shown to the Enterprise's 6,000-member crew over a two-year stretch. He said the investigation will look at "the actions of other senior officers who knew of the videos and the actions they took in response."

The Pentagon said Tuesday that Defense Secretary Robert Gates knows about the bawdy videos but is leaving the fate of Honors up to senior Navy leaders.

"The Navy leadership is fully capable of handling this issue and taking appropriate action. It is not something that requires the secretary of defense," Col. Dave Lapan, Pentagon spokesman, told an off-camera question-and-answer session.

"I don't know if the secretary has been briefed on it. I know he is aware of it," Lapan said.

He said Gates was not involved in the decision-making process over whether Honors would remain in command of the Enterprise.

CNN left a message for Honors on Saturday. The Virginian-Pilot said he did not respond to requests for comment.

The Navy issued a statement Saturday, saying, in part, "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. 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."

But the Saturday statement was an about-face from the initial military statement to the newspaper. In that statement, the Navy said the videos were "not created with the intent to offend anyone. The videos were intended to be humorous skits focusing the crew's attention on specific issues such as port visits, traffic safety, water conservation, ship cleanliness, etc."

Sims said senior officers had not yet seen the videos when they issued the first statement. It was after viewing them that the investigation was ordered, he said.

When the videos first came to light the "leadership" of the Enterprise was "directed" to make certain future videos were appropriate, the Navy said.

Sims said he was not aware if Honors was ever reprimanded. In the videos, Honors repeatedly jokes that his superior officers were unaware of the content of the videos and "they should absolutely not be held accountable."

The Virginian-Pilot says the videos were shown over the ship's internal broadcast system.

Lapan, while trying to avoid commenting directly on the Honors episode, defended how the military identifies and punishes inappropriate behavior.

"While incidents like this, allegations like this draw a lot of attention, they are still relatively few and far between in terms of the millions of service members in service doing the right thing. And we have processes in place throughout the military services to handle actions that are inappropriate or rise to higher levels," he said.

"There are always going to be people who do things they shouldn't be doing and those people will be held accountable. The system works," Lapan said.

The Enterprise videos, which include slurs against gays and lesbians, coincide with Defense Department preparations to implement last month's congressional repeal of the "don't ask, don't tell" policy that banned homosexuals from serving openly in the military.

"Those types of comments were inappropriate before the law was repealed," Lapan said.

"There's a service culture across all the services of treating everyone with dignity and respect, and inappropriate comments aren't acceptable at one point of time and unacceptable several months later because there has been a change in the law," he added.

CNN's Charley Keyes contributed to this report.