Capt. William Cogar, commander of the San Diego-based hospital ship Mercy, was found to have lied about his physical fitness and weight, the Los Angeles Times reported Friday.
Cogar, 59, was relieved of duty following an investigation by the Navy's inspector general that found "irregularities" in his records.
The Navy requires all personnel to meet certain fitness and weight standards.
Cogar took command of the ship's medical treatment facility in March.
Capt. Jeffrey Paulson, a former commander of the Mercy's hospital, was temporarily assigned to replace Cogar, who has been reassigned to the Navy Medical Center in San Diego.