An expert in US politics says Australia is not in total control of the rotation of US Marines through Darwin and warns tensions may arise in the future.

Associate Professor at the US Study Centre at the University of Sydney, Brendan O'Connor, sounded a note of caution as Darwin prepares to welcome 1,200 US Marines, who begin arriving on Monday.

"This may [have] been something that governments over a long period of time may have wanted, but when you are dealing with such a powerful ally and an ally that is so much more powerful than Australia you are not in total control of the situation," he said.

Under the deal struck between former prime minister Julia Gillard and US president Barack Obama, the number of US Marines rotating through Darwin each year will gradually increase to become 2,500 troops by 2017.

Mr O'Connor said while Australians may be in favour of the deal while Mr Obama is the US president, the agreement is a long-term deal and it may lose public support in Australia if a Republican president wins office.

"That is somewhat of the naivety of how the original deal was looked at. As a deal with Obama rather than with American politicians over a 20-year period," he said.

Mr O'Connor also was cautious about how the US troops' movements may be received by China, which is Australia's largest trading partner.

"The Chinese are pretty sensitive to the fact that American troops are coming in and out of Australia through these rotations in what is peace time," he said.

"So this is a fairly unprecedented situation."

He said that while the troop numbers were small there were also reports the US wanted a military base in Stirling in Western Australia.

"If you add all these things up, the accumulation of naval, air force activity, marine activity, I think that is how that should be looked at, in combination," he said.