Okinawan officials have expressed outrage and on Tuesday they lodged formal protests with the Marines, while the central government decided to send a senior diplomat to the island.
"U.S.-Japan relations are not just a matter of the bases," said main opposition Democratic Party leader Ichiro Ozawa.
"But (incidents concerning) military bases and Okinawa ... are likely to have a big emotional impact on the people."
However, unlike in 1995 when the Okinawa governor was a staunch critic of the bases, the current governor was elected with ruling party backing and is inclined to support Tokyo on U.S. military issues.
U.S. officials have responded quickly to mitigate fallout from the case, which comes as Tokyo tries to persuade Okinawa residents to accept a plan to relocate the Marine's Futenma Air Station from the densely populated central Okinawa city of Ginowan to the coastal city of Nago.
"Obviously, the U.S. military is cooperating with the Okinawan authorities who are investigating this," Pentagon spokesman Bryan Whitman said in Washington, adding, however, that the Marine was presumed innocent until proven guilty.
"I wouldn't tie our long-term strategic relationship with Okinawa, that part of the world to this particular incident."
The Futenma move is part of a broader plan to move some 8,000 Marines from Okinawa to Guam.
