"Effective immediately, US service members on Okinawa are restricted to base and to their residences", the announcement read.
Across mainland Japan, all US service members are also prohibited from purchasing or consuming alcohol, on or off base.
A US Marine who tested positive for excess alcohol was arrested in Japan's southern island of Okinawa on Sunday after an elderly local man was killed in a road accident, police said.
The Marine was lightly injured in the 5:30 a.m. crash in Naha, the main city in Okinawa, said Kazuhiko Miyagi of the Okinawa police. Police said the blood alcohol content of the marine was three times Japan's limit of 0.03%.
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As a result of the crash, U.S. Forces Japan has restricted all 25,000-odd U.S. service members on Okinawa to stay on their base or in their homes and has banned them from consuming alcohol.
Lt. Gen. Lawrence D. Nicholson, commanding general of Marine Forces Japan, extended his "deepest regret and honest condolences" to the Okinawan man's family. Alcohol consumption has also been prohibited by all service members on or off bases across Japan.
The Japanese driver of the minitruck, later identified as 61-year-old Hidemasa Taira, was confirmed dead at a hospital.
A statement from U.S. Forces, Japan said, "The vast majority of Soldiers, Sailors, Airmen, Marines and civilians in Japan serve honorably and make great contributions to the defense of Japan".
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The USFJ announcement, which was distributed from Yokota Air Base in Kanagawa Prefecture, added that US service personnel on mainland Japan are prohibited from purchasing or consuming alcohol on or off base.
All military members and USA government civilians in Japan are required to attend, it said.
Chief Cabinet Secretary Yoshihide Suga said Tokyo made an immediate complaint about the case to the U.S. side, demanding the United States military enforce strict discipline and take preventive steps.
That man, Kenneth Franklin Shinzato, pleaded guilty last week to raping the 20-year-old woman last year and then dumping her body, but not guilty to intending to kill her.
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Some 47,000 american troops are based in Japan, of which more than half in the small archipelago of Okinawa, where their presence is often not experienced by the inhabitants.