Australia and its close security ally the United States have been unable to resolve a payment dispute over the stationing of US Marines in Australia's northern region, in a rare stand-off blamed for delays in furthering the deployment.

The rotation of the marines through the Northern Territory was announced by US President Barack Obama five years ago as a central part of Washington's so-called "pivot" to the Asia-Pacific.

The original plan was to rotate 2,500 marines by next year as part of US efforts to increase its presence in the region to counter China's growing military clout. But now, there are just 1,250 marines in place, and the increase to 2,500 has been pushed back to 2020.

The delay follows a failure by the two sides to resolve a longstanding dispute over who will pay the final operational costs of the deployment. It is believed the amount being disputed is between A$20 million (S$20 million) and A$30 million a year during the course of the 25-year Force Posture Agreement, signed in 2014.

Asked about the dispute, Australian Defence Minister Marise Payne told The Straits Times the allies were continuing to try to ensure rotations increased to 2,500 marines by 2020. "Australia and the United States continue to work towards effectively implementing the force posture initiatives, including finalising cost-sharing arrangements," she said.

Both sides have agreed to contribute to the estimated A$2 billion to A$3 billion required for upgrading runways, accommodation and other facilities, but have been unable to agree on some of the operational costs. The final dispute reportedly centres on funding for housing and utilities like power and sewerage.

Australian officials have reportedly argued that the US presence in Darwin is different from that in Japan and South Korea, which are largely funded by the home countries. Some in Canberra have pointed to Singapore's recent agreement to pay for the upgrade of training facilities it uses in Australia.

Analyst Ashley Townshend, from the US Studies Centre at the University of Sydney, said both sides had "good intentions" but had different perspectives on the stationing of marines.

"Australia tends to think the US presence in Darwin is not the same as its presence in Japan, the Philippines or South Korea, as Australia has always been an ardent supporter of the alliance and has been involved in every major conflict that the US has been involved in," he told The Straits Times.

"Basing forces here is in Australia's interest but we have already come a long way in hosting US troops and that should be recognised. The US takes a view that… we need them more than they need us."

The unusual stand-off has played out somewhat quietly and does not appear to pose a long-term threat to the relationship. But some analysts believe it sends the "wrong message" to the region.

Mr Andrew Shearer, a former national security adviser to prime ministers John Howard and Tony Abbott who is now at the Centre for Strategic and International Studies in Washington, said the dispute was "unfortunate", especially amid growing tensions over China's show of territorial assertiveness in the South China Sea.

"Both sides need to get back to focusing on the big picture," he told The Marine Corps Times in June.

Mr Townshend said some in Canberra had noted the difference between the US approach and that of Singapore. Australia and Singapore agreed in May to expand military ties, with Singapore to invest about A$2.25 billion in defence infrastructure in Australia, where it will train up to 14,000 troops each year.

"We can't compare the two cases but it is all part of paying for regional security and shared interests."