A number of Australia's leading institutions have had United States funding for research projects paused or cut by the Trump administration, causing an outcry.
The US has also sent Australian researchers questionnaires asking if they have links with China and how their projects align with its agenda including gender policies.
"There is widespread alarm across Australian universities," National Tertiary Education Union national president Alison Barnes told AAP.
The US is Australia's largest research partner, pumping about $400 million into universities across the country last year.
The Trump administration has Australia in its sights as it moves to slash federally funded research grants across the US and the world.
The Australian National University has been the country's first major institute to confirm the US had cut funding, but a number have been targeted across the country.
Dr Barnes said it may have global ramifications, potentially impacting research for projects like vaccines that safeguard against future pandemics.
"That (Australian universities') research is so important to helping Australia, America and the world deal with ... challenges that we will face over the coming decades," she said.
"We are looking at research into vaccines being potentially adversely impacted that affects our ability to respond to future pandemics.
"I think people are very disturbed and troubled by this move."
The questionnaire issued to researchers touches on issues integral to Mr Trump's agenda including its "two sexes" executive order.
The survey poses 36 questions on topics including diversity, equity and inclusion programs, also asking whether researchers had received any funding from China, Russia, Cuba or Iran.
Other queries include what steps have been taken against "Christian persecution" or to "protect women and to defend against gender ideology."
"That Trumpist, radical, right-wing agenda runs right through that questionnaire," Dr Barnes said.
"Ideology should not influence what forms of research we invest in."
The Group of Eight represents Australia's leading research-intensive universities, receiving about 70 per cent of US funding pumped into the country's institutes.
Six of its eight institutions have been affected, Group of Eight CEO Vicki Thomson said.
"At the moment it is relatively small projects that have been targeted," she told AAP.
"But the issue is where does this lead to, when we start to think about the big research partnerships we have in defence and medical research.
"Research here and its outcomes are not quarantined to Australia, it can have impact all over the world."
Ms Thomson described the questionnaires as "completely unprecedented".
"Some of these research projects are two, three, four years in," she said.
"Now we are getting these questions which go beyond the traditional scope ... using terms like 'anti-American beliefs' and 'policies contrary to American interest'."
Dr Barnes called for the federal government to protect Australian researchers, urging universities to step up and support research grants that have been impacted.
"Research is so important to the fabric of our society. To see a right-wing ideology seeking to restrain research is really alarming."
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