A United States Defence build-up in the Northern Territory is being welcomed by local businesses and watched closely by wary northern neighbours, as some of the world's deadliest fighter aircraft arrive.

Defence analysts say the increasing presence of US Marines in the Top End is a clear sign the US is bolstering its military presence in the region, as a squadron of its sophisticated F-22 Raptors touched down near Katherine this weekend for three weeks of exercises with the Australian military.

That will soon be followed by the next rotation of US Marines and a large contingent of aircraft.

The Defence Department said it constituted the largest and longest rotation of fifth-generation aircraft to Australia to date.

Dr John Blaxland from the Australian National University's Strategic and Defence Studies Centre said it was clear "the US has a much more robust presence in Australia."

Dr Blaxland said while there was "a fair degree of assurance" the current arrangement with US troops in Darwin would remain, "in terms of the US posture in South East Asia and the region more broadly there's enormous uncertainty".

"Does this mean the US administration will take a more confrontational approach towards China, say, in the South China Sea?

"If that's the case that has potential to have significant consequences in the neighbourhood; there'll be considerable pressure on Australia to participate and to facilitate that engagement."

Chief Minister Michael Gunner said he would work hard to help local businesses seize the opportunity of Defence contracts over the coming years. "I'll be in Canberra, knocking on doors, I will be opening them, and sometimes as the Chief Minister I can open doors the private sector can't," Mr Gunner said.

The US Pacific Command says the US alliance with Australia remains strong and discussions are proceeding to send a full Marine Air-Ground Task Force of 2500 Marines to Darwin by 2020.

Major Rob Shuford, a spokesman for US Pacific Command, said: “No changes have been made to the planned rotations of Marines to Australia since the two leaders spoke.”

Major Shuford was referring to the angry exchange over the phone between US President Donald Trump and Australian Prime Minister Malcolm Turnbull about the “dumb deal” by the Obama administration to accept 1250 refugees held in offshore detention centres.

Trump’s tough rhetoric raised the prospect of a rift with Australia and sparked concerns over the future of US plans to expand its Marine presence in Darwin.

NT Chamber of Commerce acting CEO Brian O'Gallagher emphasised the importance of the US-Australia alliance to the Territory. "Hopefully this is just a hiccup and what we are seeing is nothing more than the newness of a leader who is trying to impress those people who voted him to the Presidency."

The crisis in US-Australian relations created by American President Donald Trump’s rant over a refugee deal with Australia has cast a shadow over the future of US plans to expand its Marine presence in Darwin.

Mr Trump’s threat to “study this dumb deal”, struck between Australian Prime Minister Malcolm Turnbull and the Obama Administration to take thousands of “illegal immigrants from Australia”, is a further warning that none of the previous agreements between Australia and America are safe from change.

Mr Trump has made no secret of the fact that he believes US allies should pay more to host American military contingents. A cost-sharing arrangement between the two nations was only struck in October after months of to-and-fro, despite former president Barack Obama’s enthusiasm for the deal. The agreement with the Obama administration would see the number of Marines stationed in the NT increase to 2500 by 2020.

Mr Trump’s apparent willingness to abandon promises made by his predecessor puts this on shaky ground.

The effects of any downsizing of the planned US Marine deployment would have a significant impact on a Territory economy. which is already suffering duress.

The NT is relying on an increased defence infrastructure spend, including a $2 billion investment as a direct result of the Marine rotation, to tide over the economy as the Inpex construction phase ends.

Chief Minister Michael Gunner said the deal as it stood would provide a “significant economic boost” to the Territory.

However, he emphasised that the Australian Government had already committed to spending billions on defence in the Territory.

“I strongly disagree with many of President Trump’s views, actions and decisions,” he said.

“However, the NT’s relationship with the US is a long and enduring one and goes beyond the views and actions of a single President or Chief Minister. It is crucial to gaining important economic investments, most notably through defence spending and the placement of US Marines.”

Member for Solomon Luke Gosling agreed saying he was confident the deal would stay.

“You cannot underestimate the value of this defence co-operation and constructive United States engagement in our region,” he said.

Mr Gunner said despite President Trump’s behaviour an invitation to visit the Territory still stands.

U.S. and Australian troops have been fighting together since World War I, but President Trump’s recent spat with Australia’s prime minister underscores that cooperation between the two countries has not always been easy.

Since 2012, the U.S. has rotated a small force of Marines through Darwin, Australia. Both countries had hoped to send a full Marine Air-Ground Task Force of 2,500 Marines to Australia by 2016, but that timeline has been pushed back to around 2020.

The plan fell behind schedule amid negotiations between the two countries about who should pay to build the infrastructure for the extra Marines, said Andrew Shearer, a former Australian defense official.

“There was quite a long delay — 18 or 20 months — to conclude a cost-sharing agreement,” said Shearer, with the Center for Strategic and International Studies think tank. “Those cost-sharing negotiations, which were difficult — and I think a little bit acrimonious at officials’ level — that was concluded last October.”

In addition to disagreements about money, some U.S. officials felt the cost-share arrangement should mirror arrangements with other allies, such as South Korea and Japan; while Australian officials objected to applying a “cookie cutter model” to their country, he said.

“Even close allies have pretty tough negotiations with each other over this sort of burden-sharing,” Shearer said. “I think negotiations just got off to a slightly bad start. I think that, frankly, there wasn’t enough political push from both sides to get their officials to get the thing over the line sooner.”

Currently, both countries are assessing how much construction is needed at Robertson Army Barracks in Darwin and Royal Australian Air Force Base Darwin, Shearer said.

“Now they’re up to where — in my view, frankly — they should have been 12 or 18 months ago,” he said.

Australia is a key ally and was a major part of the Obama administration's effort on the Asia-Pacific region. But the so-called “pivot to Asia” ended up being more symbolic than substance as threats in the Middle East re-emerged.

The latest rotation to Darwin begins in April and will involve 1,250 Marines, mostly from 3rd Battalion, 4th Marines, based at Camp Pendleton, California, said Chuck Little, a spokesman for U.S. Marine Corps Forces, Pacific.

The Marines are also sending the most aircraft to Australia since the rotations there started, Little said. The aviation combat element will be made up of four MV-22B Ospreys from Marine Medium Tiltrotor Squadron 268; along with five AH-1W Super Cobra and four UH-1Y Venom helicopters from Marine Light Attack Helicopter Squadron 367. Both squadrons are based at Marine Corps Air Station Kaneohe Bay, Hawaii.

Little confirmed that the U.S. and Australia are reviewing how much infrastructure needs to be added to Robertson Army Barracks and RAAF Darwin to accommodate 2,500 Marines and their aircraft.

There is no set time line yet for when an entire Marine Air-Ground Task Force will rotate through Australia

Recent changes to the US National Security Council should be ringing loud alarm bells in Canberra.

By demoting the highest-ranking military officer and the highest-ranking intelligence officer, and appointing political adviser Stephen Bannon as a permanent member of the NSC, Donald Trump has seriously escalated the risk of the US launching into ill-advised conflicts. Bannon comes from a role as chairman of the racist, Islamophobic website Breitbart.com, and is reported as having been in charge of writing the recent executive order that has banned US entry for refugees and citizens from seven Muslim-majority nations.

It is no secret that Australian foreign policy and defence forces are closely enmeshed with the US. Since Trump has taken office he has loudly proclaimed an "America first" foreign policy, and his Secretary of State, Rex Tillerson, talks of denying China access to artificial islands in the South China Sea. Any such blockade is likely to be seen by the Chinese as an act of war.

Malcolm Turnbull's meek response to the immigration executive order does not inspire confidence that he will stand up to the US.

Historically Australia's foreign policy has also leaned towards "America first", with little differentiation between our ally's interests and our own. In rushing to join the coalition going into Iraq, the thought that Australia may be better off not invading another country on the basis of dubious intelligence was overlooked. Indeed, in the Vietnam War, the CIA knew the war was unwinnable, even before Australia sent troops. Malcolm Fraser, defence minister at the time, was livid when he discovered this many years later. A total of 521 Australian troops died in Vietnam and about 3000 were wounded.

Since World War II, Australia has joined in more US wars than any other ally. With Canberra's current "business as usual" agenda, Australia is at high-risk of joining future US wars that will likely create further humanitarian disasters and undermine our security.

Simultaneously there is talk of expanding US bases in the region. What is Australia going to say when the US asks to increase its bases on our soil? Are we willing to make Australia a target? CIA documents from the 1980s released this month revealed authorities expected the Pine Gap spy base near Alice Springs to be attacked in the event of a US-Soviet nuclear fight.

Australia has US marines based in Darwin, multiple surveillance bases and about 40 senior Australian Army officers working in US Pacific Command. This includes an Australian Army Major-General serving as the deputy commanding general – operations, US Army Pacific. This intense enmeshment reinforces Australia's past behaviour; when the US goes to war, we have little option but to follow. With the US building up its military bases around China, American threats of blockades in the South China Sea are reckless and provocative. A war between China and the US is not in Australia's interests or anyone's interests.

Another example of US influence has been Australia's behaviour at recent UN talks regarding the nuclear weapons ban treaty. Australia has acted as US proxy in trying to thwart these negotiations. So much so that the Australian delegation was dubbed the chief of the "weasel states". Despite Australia's efforts, negotiations for a treaty will go ahead this year. Australia has not committed to participating, which calls into question our government's commitment to the UN.

Australia urgently needs to re-evaluate its American bases and promote steps that defuse rather than intensify regional tensions. Having senior Australian defence personnel integrated into the US defence force hinders Australia acting independently. Do we want Australia to be capable of making strategic decisions in the national interest? New Zealand clearly acts in its own interest and remains an ally.

With Trump now the new US Commander-in-Chief, is it wise that we allow ourselves to be so automatically tied to American foreign policy? War in our region would be a humanitarian catastrophe for all involved.

Margaret Beavis is a Melbourne GP and president of the Medical Association for Prevention of War.