The first contingent of United States troops to be deployed in northern Australia under a new bilateral defence deal landed in Darwin last night to start a six-month rotation.

About 200 US Marines from the Hawaii-based Fox Company, 2nd Battalion, 3rd Marines were welcomed by Defence Minister Stephen Smith when they arrived at Darwin Airport on a charter flight just before midnight.

The unit has recently been involved in active service in Afghanistan.

The Marines are in the Top End on a six-month rotational basis and will undertake joint training exercises with the Australian Defence Force.

They will be based at Robertson Barracks on the outskirts of Darwin.

The infantry company will use ADF training areas at Mount Bundy and Kangaroo Flats and will also spend two months away from the Northern Territory, working in some of the US "partner countries" in the region.

The Marines are the first contingent of 2,500 US troops to be deployed in northern Australia by 2017 as part of a deal announced by US president Barack Obama during his trip to the Top End last year.

Mr Smith says Darwin and the Northern Territory have welcomed the arrivals.

"The Northern Territory's got a longstanding history of working closely not just with the Australian Defence Force, but also with the United States," he told Radio National's Breakfast program.

"I think the mood here is one of very strong enthusiasm."

He says as the rotation is staged, the Government will be ensuring there are no problems for the people of Darwin.

At the time of the deployment announcement, Indonesia expressed concern that basing US Marines in northern Australia could inflame tensions in the region.

But Mr Smith says that was not the view expressed by Indonesian president Susilo Bambang Yudhoyono.

"He saw the prospect of not just Australia, the United States and potentially Indonesia engaging in exercises, but also the wider region, including China," he said.

"When that suggestion was made, both the US ambassador and I publicly welcomed that suggestion and said in due course that could be something that we could work towards."

Mr Smith will join an official welcome at Robertson Barracks later this morning.