Navy Capt. Greg Thomas, who was lauded in 2010 for helping turn around Pearl Harbor Naval Shipyard and was selected for promotion to rear admiral, was reprimanded Tuesday and permanently relieved of command at Norfolk Naval Shipyard in Virginia, his follow-on assignment.

Naval Sea Systems Command Vice Adm. Kevin McCoy reprimanded Thomas for violating Article 133 of the Uniform Code of Military Justice, conduct unbecoming an officer and a gentleman, the command said.

The action was based on "substantiated allegations from a formal investigation by the Naval Inspector General into the command climate and Thomas’ treatment of subordinates under his command," the Navy said.

He was permanently relieved of command of the Norfolk shipyard and reassigned to administrative duties.

Thomas took command of the East Coast shipyard in September 2010. On May 25 he was assigned to temporary duty in Washington, D.C., at Naval Sea Systems Command headquarters pending completion of the investigation.

In September 2010, when he left Pearl Harbor shipyard as commander, Thomas received a Legion of Merit award from McCoy for exceptionally meritorious service during three years as shipyard commander.

"The past three years under Greg Thomas’ watch have been terrific," McCoy said at the change of command.

"The Navy does not select admirals based on their superb performance to date. The Navy selected you as an admiral, Greg, based on what we know you will do for our nation in the future, and we absolutely picked the right man," McCoy said.

Thomas was known as being demanding and tough with high standards, but also as a fair commander who liked to talk to shipyarders and praised good work.

He was picked in 2007 to help turn around Pearl Harbor shipyard’s efficiency problems and prepare the way for new Virginia-class subs. Submarines represent 90 percent of the shipyard’s work.