Command Master Chief Adrian McCown has been temporarily reassigned to the staff of Naval Surface Group Middle Pacific, the service said.
"Those (equal opportunity) complaints prompted the investigation, which is ongoing, but the fact that the investigation is being done has led to a loss of confidence, which is what led to the release," said Lt. Rebecca Haggard, a spokeswoman for Naval Surface Force U.S. Pacific Fleet in San Diego.
Haggard said the equal opportunity complaints were lodged by ship crew members. She added that the investigation was initiated following those complaints "and some other allegations."
McCown was relieved of his duties Friday by the commanding officer of the Michael Murphy, Cmdr. Todd E. Hutchison, "due to a loss in confidence in his ability to perform the duties as command master chief based on an ongoing command investigation into alleged misconduct and command climate," the Navy said.
McCown was considered part of the "triad" of ship leadership that includes the commanding officer, executive officer and command master chief.
Master Chief Petty Officer Jamison Meyer, a fire controlman, will assume temporary duties as the senior enlisted adviser on the Michael Murphy, the Navy said.
McCown enlisted in 1994 in Houston, according to his ship biography. His first sea duty assignment was aboard the USS Rodney M. Davis. Other ship assignments included the USS McFaul, USS John S. McCain and USS Lassen. He also served with the Navy Military Police Guard Battalion in Parwan, Afghanistan.