The threat came in at 3:58 p.m., targeting a barracks for single sailors near the Personnel Support Detachment building.
Commander Fleet Activities Yokosuka
U.S. military bases reported minimal damage after a full day hunkered down against record-breaking rain and strong wind.
Authorities urged U.S. military personnel and their families at bases on the Kanto Plain to stock up and sit tight.
It was Cindy McCain's first visit to the warship that bears her late husband's name since the Arizona senator's death.
Commands and units have the option of wearing an embroidered shoulder patch on the Navy Working Uniform Type II and III.
The request to "minimize visibility" of the destroyer McCain came from a junior White House staffer.
The president and the acting defense secretary distanced themselves from an order to keep the ship out of sight on a visit.
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.