The U.S. government-funded Voice of America quoted local police as saying the Marine's blood-alcohol level registered three times the legal limit during a breath test.
Nicholas James-McLean, 21, was arrested on the island on Sunday after being suspected of driving under the influence of alcohol.
The U.S. military has banned all soldiers stationed in Japan from drinking alcohol.
US troops in Japan are not allowed to buy or consume alcohol both on or off base, following a deadly auto accident involving a US service member who may have been under the influence of alcohol, the US Forces in Japan said in a statement.
A small truck driven by Hidemasa Taira, 61, was making a turn at about 5:30 a.m.at an intersection in Naha when it was hit by an Isuzu Elf driven by James-McLean coming from the opposite direction, the spokesman said.
The truck driven by James-McLean was a USA military vehicle. All Japan-based servicemembers are prohibited from purchasing or consuming alcohol on or off base until further notice. According to witnesses cited by local media, the crash occurred after the military truck ran through a red light. The governor has long cited accidents and crimes committed by USA servicemen in his demands to alleviate Okinawa Prefecture's burden of hosting the bulk of US military bases in Japan. The police told Stars and Stripes that they were investigating the incident, but declined to comment if USA personnel had been targeted. The main causes for objection include jet crashes related to the United States bases as well as sexual assaults and other crimes linked to USA military personnel.
The military said commanders across Japan will immediately lead mandatory training on responsible alcohol use and acceptable behavior.
"The Defence and Foreign Ministries have lodged a stern representation to the US forces in Japan and the USA embassy in Japan, asking for the enforcement of discipline, prevention of recurrence and honest response to the bereaved", Japanese Chief Cabinet Secretary Yoshihide Suga told a regular news conference on Monday.
A total of 29 civilian vehicles owned by U.S. personnel in Japan were covered with paint early on Monday in the towns of Ginowan and Chatan in Okinawa, Stars and Stripes, the official USA military newspaper, reported.
U.S. Ambassador to Japan William Hagerty expressed his condolences and offered an apology, Suga said.
There are around 100,000 United States military personnel now in Japan, with half of them stationed in Okinawa, according to the USFJ website.
Obama, who was visiting Japan for a Group of Seven summit, expressed "deepest regrets".
In Okinawa, personnel are also restricted to base or to their residences.
The case is under trial.