Japanese ministers give their reaction to a deal involving the relocation of 9,000 US military personnel Reuters

Japan and the US have agreed to relocate thousands of US marines from Okinawa in a move aimed at reducing the island's military burden amid lingering anger among residents over pollution, accidents and crime.

Under a deal reached in Washington late on Thursday, about 9,000 marines will move from the southern Japanese island to the US Pacific territory of Guam and other locations in the region, including Hawaii and Australia.

By shifting a large number of the 19,000 marines on Okinawa, leaders in Tokyo and Washington said they hoped to reduce the US military footprint on the island while retaining a strong enough presence to deal with security emergencies in the region.

In a joint statement, the US defence secretary, Leon Panetta, and the secretary of state, Hillary Clinton, said the agreement would honour Washington's commitment to defending Japan and maintaining stability in an "increasingly uncertain security environment".

"Japan is not just a close ally, but also a close friend," Panetta said separately. "And I look forward to deepening that friendship and strengthening our partnership as, together, we address security challenges in the region."

No date has been given for the $8.6bn (£5.3bn) move – of which Japan will pay $3.1 billion – and questions remain over the fate of Futenma, a sprawling marine base located in Ginowan, an Okinawan city of 95,000 people.

Earlier this year, President Obama signalled a shift in US military priorities towards the Asia-Pacific region, after a decade of prioritising expensive wars in Iraq and Afghanistan.

The potential for volatility in east Asia was underlined by North Korea's recent rocket launch and the prospect of a third nuclear test by the regime.

There is concern, too, over Beijing's military spending and long-standing disputes between China and Japan over territory and energy resources.

"I think we have made some progress and this plan offers specific and forward-looking action," said Japan's foreign minister, Koichiro Gemba, adding that Japan wanted to "reduce the burden on Okinawa".

But the agreement, made days before the Japanese prime minister, Yoshihiko Noda, meets Obama in Washington, is unlikely to satisfy residents living near Futenma, a cause of friction between successive US and Japanese administrations.

Local opposition to the US military presence on Okinawa reached a high point in 1995 after three servicemen abducted and raped a 12-year-old girl.

The crime prompted the US and Japan to look for ways to reduce the military presence on Okinawa, which comprises less than 1% of Japan's total area, yet hosts three-quarters of all US bases and just under half its 47,000 troops.

The talks led to a 2006 agreement under which Futenma was to be relocated to Henoko in a less populated part of Okinawa, and 8,000 troops moved off the island by 2014.

The Futenma question remains unresolved, however, after the government in Tokyo failed to persuade people in Henoko – an ecologically important stretch of coastline – to agree to host the new offshore base. Most residents of Okinawa want the base moved off their island altogether, but the government has failed to find a new host community.

Up to 5,000 troops – about 3,000 fewer than envisaged in the original 2006 agreement – will be sent to Guam, according to a US defence official quoted by Associated Press in Washington. The remainder will move to Hawaii or rotate between Australia and other parts of the region.

Kurt Campbell, the US assistant secretary of state for east Asian and Pacific affairs, said the deal should satisfy congressional critics who had denounced the original plan as confused and expensive.

"We think it breaks a very long stalemate that has plagued our politics, that has clogged both of our systems," he said.