Scientists at the CSIRO have been sent a questionnaire from the Trump administration asking about policies on diversity, gender ideology, and whether "climate justice" is part of their remit.
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It follows similar questionnaires to a string of prominent Australian universities, including the Australian National University, which said it had lost American funding.
"CSIRO has a number of touchpoints with the US government as part of our research portfolio," a spokesperson for the CSIRO said. "We are aware of a small number of researchers who have received a questionnaire, and we are determining an appropriate response."
The CSIRO said it had not been told of any cut in funds so far: "As the situation is still developing, it would be premature to speculate on how the changes in the US will affect CSIRO's US collaborations and partnerships. However, CSIRO has not received formal advice that our science collaborations will be impacted."
It follows the cutting of funds to the ANU because of what Mr Trump and his followers perceive as a "woke agenda". The ANU was the first - and so far only - Australian entity to acknowledge losing money because of pressure from Washington.
Its vice-chancellor Genevieve Bell told staff: "We have had the first termination of funding from the United States."
The "termination of funding" revelation came after the Trump administration sent its 36-question form to at least eight universities in Australia as well as to the CSIRO.
It mirrored that sent to American universities, some of which have subsequently had their funding cut by hundreds of millions of dollars.
Apart from the questions on whether any departments or staff "defend against gender ideology", and whether they had policies promoting "diversity, equity and inclusion", there were questions on whether academics had links to China and to terrorism.
One question asks: "Can you confirm that your agency has not collaborated with, had any accusations or investigations of working with an entity on the terrorism watch list, cartels, narco/human traffickers, organised or groups that promote mass migration in the last 10 years? [yes/no]."
The Australian Academy of Science said the government should "give serious and urgent attention to recent actions by American authorities".
"If responses to the survey lead to reductions or cessation of US-Australian scientific collaborations, it will directly threaten our scientific and technological capability and diminish Australia's strategic capability in areas of national interest such as defence, health, disaster mitigation and response, AI and quantum technology."
The Academy of Science said that US government funding involving Australian research organisations added up to $336 million.
The main union at the ANU urged the federal government to protect Australian researchers from foreign influence.
"The federal government must push back on the Trump administration's blatant foreign interference in our independent research in the strongest possible terms," Alison Barnes, president of the National Tertiary Education Union, said.
"A foreign government seeking to destroy public education globally must have zero influence on what Australian researchers and their international colleagues work on.
"Donald Trump's hateful agenda is racist, transphobic and misogynistic. The idea of research funding being tied to any of those values is sickening."
