The 20-year-old was held for alleged negligent driving resulting in death, said Kazuhiko Miyagi, a road traffic officer with Okinawa police.
A 61-year-old Japanese man was killed when his vehicle collided with the serviceman's truck at an intersection.
A breath test on the Marine showed an alcohol level three times the legal limit, Miyagi said.
The US Marine Corps confirmed the accident in a statement, expressing "sincere condolences" to the family of the dead man and promising full cooperation with the investigation.
But crimes by US personnel have been a frequent irritant in relations.
In the most recent case, a former US Marine employed at the US Air Force's sprawling Kadena Air Base on Okinawa was charged with the murder of a 20-year-old woman in April last year.
The case intensified longstanding local opposition to the American military presence on Okinawa.
The island accounts for nearly 75 per cent of land allotted for US bases in Japan even though it has a fraction of the country's total area.
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