WASHINGTON — The Navy has fired the commander and the second in charge of the littoral combat ship Montgomery because of “a loss of confidence in their ability to command,” the service said Thursday.

Cmdr. Richard J. Zamberlan, the ship’s skipper, and Cmdr. Phillip Lundberg, the vessel’s executive officer, were relieved by Capt. Marc Crawford, the commander of the Navy’s Surface Division 11, the Navy said in a statement.

The Navy did not elaborate on the circumstances of the firings, but two Navy officials said the officers’ removal had resulted from their handling of a sexual harassment investigation. The two officials spoke on the condition of anonymity because of the continuing inquiry.

It is unusual for the Navy to relieve a ship’s commander, much less its two top officers, for any reason. In April, the Navy removed Cmdr. Kathryn J. Dawley as the skipper of the Hawaii-based guided-missile destroyer Hopper for what officials said was a poor command climate and bad crew morale.

In the case of the San Diego-based Montgomery, Zamberlan and Lundberg will be reassigned to desk jobs at the headquarters of the Pacific Fleet’s Naval Surface Force. Cmdr. Dustin Lonero, from the littoral combat ship Coronado, was assigned as the Montgomery’s skipper until a permanent replacement is named.

The Navy has dealt with other command issues related to sexual harassment in recent months. In April, the admiral in charge of naval aviation maintenance depots, Rear Adm. Trent DeMoss, was removed from command pending a Navy inspector general inquiry into sexual harassment complaints. That firing was reported earlier by USNI News.

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Littoral combat ships like the Montgomery are a relatively new class of Navy warship. They entered the fleet in the past two years to operate in littoral areas, or waters close to shore, where larger vessels may have difficulty maneuvering.

Small and agile with crews of about 80 sailors, Independence-class littoral warships like the Montgomery have a futuristic-looking, all-aluminum trimaran design. The Montgomery has in recent years patrolled contested waterways like the South China Sea and the Philippine Sea in what Navy officials say is a signal to allies and adversaries that the United States is committed to protecting free and open international waters.

The littoral combat ships have experienced growing pains, with engine problems and other flaws that Navy officials now say they have ironed out.