Residents have complained for years about noise, pollution and crime around the bases. Japan and the US signed a pact in 2006 that called for the realignment of American troops in the country and for a Marine base on the island to be moved to a less populated area. But the new Tokyo government is re-examining the deal, caught between increasingly adamant public opposition to American troops and its crucial military alliance with Washington.
On Saturday, labour unionists, pacifists, environmentalists and students marched through central Tokyo, yelling slogans and calling for an end to the US troop presence. They gathered for a rally at a park - under a banner that read "Change! Japan-US Relations" - for speeches by civil leaders and politicians.
Prime Minister Yukio Hatoyama has repeatedly postponed his decision on the pact, with members of his own government divided on how to proceed. Last week he pledged to resolve the conundrum by May, just before national elections. "The Cabinet is saying that it will announce its conclusion in May. For this reason, over the next few months we must put all of our energy into achieving victory," Cabinet minister Mizuho Fukushima said at the rally, to shouts of approval from the crowd.
Fukushima - who has a minor post in the Cabinet and heads a small political party - wants the base moved out of Japan entirely. Hatoyama's government must appease such political allies to maintain its majority coalition in parliament, and the public are increasingly vociferous on the US military issue, even outside of Okinawa.
"I'm against having troops here. I'm not sure we can get them all out, but at least some of them should leave," said Seiichiro Terada, 31, a government tax collector who attended the rally. Terada said he travelled from his home in the central prefecture of Shizuoka, which hosts a Marine base at the foot of Mt. Fuji.
The deal with Washington calls for the Marine base in a crowded part of Okinawa to be moved to a smaller city called Nago. But last week residents of Nago elected a new mayor who opposes the move, ousting the incumbent that supported a US military presence.
On the other side of the debate, a steady stream of US officials have petitioned Tokyo to follow the agreement and maintain American troop levels in Japan, with US Ambassador John Roos on Friday calling them "front-line forces" in case of emergencies or security threats.