Lateline has obtained unofficial minutes of a CSIRO staff meeting last month, where one researcher directly raised the United Nations Development Program's concerns about funding the organisation in future.
"The UN told him that in their view, the new CEO was not reliable," retired CSIRO fellow Dr Nick Abel said.
"And they were frightened that if they did hand over a lot of money to CSIRO under contract, there was a danger that he might cancel those contracts and leave them with the ultimate embarrassment for the UN, which is millions of dollars of unspent money."
Billions of dollars worth of grants were pledged for climate research and mitigation at the Paris climate talks last year.
Lateline has spoken to a number of scientists who fear the CSIRO's new innovation and industry focus is leading to a "dramatic reduction" in "public good" science.
Dr Abel pointed to the biological control of rabbits through Myxomatosis in the 1950s, and Calicivirus 30 years later.
"They were hugely economically beneficial. And the Government paid for it, CSIRO did it. No company's going to do that," he said.
"What company would get into the virology research that's going to produce that kind of benefit because they can't capture the revenue from the farmers because the thing spreads?
"It is a plague and spreads like one and kills the rabbits and no company can say: 'Hey, we did it. We've come to collect your payment for it.'"
The change is being driven by Mr Marshall, who was appointed under Tony Abbott after spending 25 years as an entrepreneur in the United States.
Mr Marshall's vision for the organisation is focused on getting financial returns for the funding it receives.
In emails between managers released after a Senate inquiry request, it was made clear "public good" research — a mainstay of CSIRO in decades passed — is no longer in favour.
"Public good is not good enough, [it] needs to be linked to jobs and growth," one email from deputy director of the oceans and atmosphere business unit, Andreas Schiller, said.
Dr Abel said: "I've become convinced in the absence of any financial arguments within CSIRO, economic arguments in relation to Australia, social arguments in relation to our nation, that it is ideologically driven."
"A 100-year-old organisation that was the national pride of Australia is turning into a national embarrassment."
In a statement, CEO Larry Marshall said: "Science in the national interest is absolutely our mandate, and we are not changing this."
"We're absolutely committed to continuing our public good research. I believe CSIRO is the best organisation in the nation to map the path to prosperity, sustainability, and societal benefit.
"Our climate science is part of this, as also are research in other areas.
"Australia's economy is in transition and unless we help the nation prepare for the changes ahead — for digital disruption and for the massive shifts in the way we work and live — our productivity and quality of life will fall."
Australia 'reneging' on Paris agreement, ex-CSIRO manager says
Research manager Dr Peter Craig retired from the CSIRO just over two weeks ago.
He believes as well as the loss of reputation and capacity, Australia is also at risk of breaching commitments made at last year's climate talks in Paris.
"The COP21 agreement actually requires an increase in climate science, not a decrease in climate science," he said.
"Within months of the agreement being reached in Paris, Australia is reneging on the agreement."
Mr Marshall explained the move in an email to staff in February by describing climate science as "proven".
"That question has been answered, and the new question is what we do about it, and how can we find solutions for the climate we will be living with," he said.
Dr Craig is no longer gagged by any employment agreement.
"[It's] a transparently false reason for stopping climate science. Somebody compared it with cancer research," he said.
"We know what cancer is, we can stop cancer research. It makes no sense whatsoever."
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