The United States and Japan said Thursday Tokyo would pay a third of the cost of Washington pulling thousands of Marines out of Japan as it reduces its heavy military presence on Okinawa.

US Secretary of State John Kerry, Secretary of Defense Chuck Hagel, Japan’s Foreign Minister Fumio Kishida and Defense Minister Itsunori Onodera signed the protocol amending the 2009 Guam International Agreement, as part of a meeting on the two countries’ alliance.

Changes include “clarifying that Japan will contribute up to $3.1 billion in Fiscal Year 2012 US dollars in direct cash contributions to develop facilities and infrastructure in Guam and the Commonwealth of the Northern Mariana Islands”, the state department said.

It accounts for 36 percent of the projected $8.6 billion cost of the relocation.

In a 2012 agreement, the United States said it would pull 9,000 Marines out of Okinawa — 4,000 of whom would go to Guam and 5,000 to Hawaii and on rotations to Australia — as it seeks to ease a long-running standoff over the future of its huge military presence in one of its top Asian allies.

The US is beefing up its military assets across Asia, with Australian bases soon to host some of its most formidable strategic weapons.

A US defence official said American B-1 bombers were bound for Australia as a deterrent to what they described as China's "destabilising effect" in the region.

The move is part of the Obama administration's plans to "assert freedom of navigation" in the South China Sea.

Assistant US defence secretary David Shear confirmed the move.

"We will be placing additional air force assets in Australia as well as B-1 bombers and surveillance aircraft," he said.

China's foreign ministry expressed "serious concern".

The US air force said the B-1 bomber was the back bone of its long-range bomber force

Mr Shear told a special congressional hearing on the South China Sea the deployment of air assets to Australia was in addition to the doubling of US marines bound for Darwin, leaving their current base in Japan. "We will be moving significant numbers of Marines to Hawaii, Guam and Australia," he said. "So we will have a very strong presence, very strong continued posture throughout the region to back our commitments to our allies, to protect and work with our partners and to continue ensuring peace and stability in the region.

The Marines will be stationed in Darwin for training for the six months of the Top End's dry season. They are the fourth rotation since former prime minister Julia Gillard and US president Barack Obama struck a deal in 2011 to gradually increase the number of US Marines rotating through Darwin to 2,500 troops by 2017. A small ceremony was held at Darwin Airport with America Galaxy C5 as aircraft carrying CH-53E Super Stallion helicopters from Guam in Central America touched down. "We're coming from all over the globe," Lieutenant Colonel Eric Dougherty of the US Marine Corp said. He described the rotation in which US Marines will live and train at the Australian Defence Force's Robertson Barracks as "unique". "Most places we go to a different country and have our own base there. We're operating inside the base," he said. "But here we're going to be living inside the barracks. "You guys have opened up your homes to us. We're living in your guest house." Lt Col Dougherty said the training opportunities in the Northern Territory were a big drawcard. "You have some world-class training facilities here," he said. "Bradshaw training area (south-west of Darwin) is three times the size of anything we have in the States. "The outback truly is out back, with vast wide open spaces. "There's things we can do here we cannot do back in the States."

The rotation follows speculation the growing US military presence in Darwin could cause tensions with China. Lt Col Dougherty would not comment on what impact another rotation of US Marines would have on relations with China. Last year for the first time Chinese soldiers trained on Australian soil with the Australian Army and US Marines, but Lt Col Dougherty said no training was planned with China on this rotation. He said the Marines were keen to start sporting teams, including trying their hand at rugby union.

With a GDP per capita less than a third the US average, an earthquake-damaged harbor, geriatric generators that black out the entire island roughly twice a year, drinking water periodically contaminated with sewage, a fire department with three working ambulances for a population of 160,000, and a police department so short-staffed it’s started deputizing unpaid civilians ...

the Pentagon’s still rewriting its Guam plan. The original goal was to relocate 8,600 Marines and 9,000 dependents from Okinawa to Guam by 2014, but disagreements over cost-sharing with the Japanese led the Defense Department to scale the move down to 5,000 Marines and 1,300 dependents.