Rear Adm. Jeffrey Harley told Stars and Stripes the crew of the USS Guardian will remain together at home port in Japan and train for "potential assignments" until further notice.
Their commanding officer, Lt. Cmdr. Mark Rice, and other technical experts remain on U.S. vessels near the Guardian to assist in salvage efforts.
No one was injured when the Avenger-class ship ran aground on Jan. 17 while transiting the Sulu Sea after a port visit in Subic Bay.
Harley said every hazard to the environment has been removed from the Guardian and stabilization is under way.
The ship ran aground on Tubbataha Reef, a protected World Heritage Site.
An investigation into the incident is ongoing.
The Navy said the Guardian may remain on the reef for as long as two weeks until heavy-lift ships arrive from Singapore.