The president and the acting defense secretary distanced themselves from an order to keep the ship out of sight on a visit.
Commander Fleet Activities Yokosuka
Navy officials said they had identified misconduct during an ongoing investigation.
Five are still missing after a KC-130 Hercules and F/A-18 Hornet collided during routine refueling training off Japan.
The USS Ronald Reagan returned to its Yokosuka homeport after spending nearly four months patrolling the Western Pacific.
Japanese police have accused a 24-year-old USS Ronald Reagan sailor of smuggling drugs into the country.
As court proceedings open on Tuesday, the Navy will begin hashing out what went wrong and who should be held accountable.
A cost-of-living survey that's about to do the rounds at bases in Japan could impact allowances that were slashed earlier.
The sailors, some assigned to the carrier Ronald Reagan, are suspected of buying, selling and using illegal drugs.