The United States is to shift 9,000 Marines out of Japan in a move Washington hopes will ease sometimes fractious relations with its ally over a huge American military presence.

The redeployment, which will see troops moved to Guam, Hawaii and Australia, will go ahead regardless of any progress on the moving of a busy airbase on Okinawa that had originally been a key plank of a deal with the US.

In a joint statement issued in Washington and Tokyo, the two sides said they remained committed to the relocation of the Futenma base from its present urban location to a coastal spot -- a move that is heavily resisted in Okinawa.

The two governments "reconfirmed their view that (this) remains the only viable solution that has been identified to date", the statement said.

No definite timeframe was put on the redeployment, with the statement saying only that the "relocations are to be completed as soon as possible while ensuring operational capability throughout the process".

Japanese Foreign Minister Koichiro Gemba said the agreement was necessary to reflect an evolving regional reality.

"Changes in the security environment will not wait for us. Japan and the United States have to assume our responsibility and do our part and implement the plans in a speedy manner," he told reporters in Tokyo, amid growing unease over the rise of China.

"The (base-move) problem brought everything to a halt. We must make progress where we can."

The deal comes just ahead of a visit to Washington by Prime Minister Yoshihiko Noda, who will meet with President Barack Obama on Monday for what both sides hope will be a demonstration that the alliance is back on track.

Japan and the United States have long clashed over Okinawa, the site of sporadic tensions with US troops. Around half of the 47,000 US service personnel in Japan are based on the strategically located island, which is nearer to Taiwan than it is to Tokyo.

In the never-implemented 2006 deal, the United States agreed to shift the Futenma air base -- a longtime source of grievance as it lies in a crowded urban area -- to a quiet stretch of seashore, with 8,000 Marines leaving Okinawa for Guam.

But some activists in Okinawa pressed for the base to be removed completely. The controversy felled one Japanese prime minister, Yukio Hatoyama, who failed to fulfil campaign pledges in 2009 to renegotiate the deal.

Speaking ahead of the official announcement, Kurt Campbell, the Assistant Secretary of State for East Asian and Pacific Affairs, said the deal would move relations forward.

"We think it breaks a very long stalemate that has plagued our politics, that has clogged both of our systems, that has made it difficult to deal with the critical and crucial issues that confront the United States and Japan," Campbell said.

The announcement comes after the two sides said they were decoupling the marine redeployment from the base-move issue, which is likely to remain mired in the sticky interface between Okinawa and Tokyo.

A senior state department official said the delinking had allowed things to move forwards.

"Previously everything was a package, until we had progress on constructing the Futenma replacement facility, we weren't doing a lot of other things," said the official, who requested anonymity, in line with usual policy.

"One of the key aspects of this agreement is that we're separating the piece of constructing a replacement facility for Futenma from the other aspects of the agreement because we're acknowledging it's taking more time than we anticipated."

The statement said the total cost of the relocation to Guam was expected to be $8.6 billion, with the US official saying more than a third would be paid by Tokyo.

"The $3.1 billion dollar Japanese cash commitment... is significant and we particularly appreciate this commitment in the context of Japan's fiscal challenges, which we fully recognise," the defence department official said.

Around 5,000 of those leaving Okinawa will be heading to Guam, with the remainder going to Hawaii and Australia where Washington is "establishing a US Marine Corps rotational presence", the statement said.

"In executing these moves, the US government reaffirmed its commitment to sustain its current military presence and enhance military capability in the Western Pacific."

The agreement is part of a wider US strategy under President Barack Obama who is pushing to re-engage with Asia and reconfigure the American military presence in the region amid concerns over China's rapid rise.