Leaked emails from 2015 reveal a bitter dispute within CSIRO, Australia's leading science body, as management tried to prevent top scientists from breaking ranks before the Paris climate summit.

The disagreement took place after CSIRO declined to make a formal submission to a government consultation about Australia's new emissions target.

The emails detail internal concerns that, at key moments dating back to 2009, the organisation had been "missing in action" in providing advice on climate change, and that it should not be trying to "operate behind closed doors" with government.

Critics say these tensions between CSIRO management and scientists are a symptom of ongoing self-censorship by an organisation fearful of offending government and losing funding.

But CSIRO has defended its actions, arguing it is fully engaged in advising government and contributing to policy debates on climate change.

Spokesman Huw Morgan said that in some instances CSIRO avoided contributing to specific inquiries because of their policy focus and the organisation's desire not to "advocate, defend or publicly canvass the merits of government or opposition policies".

CSIRO has guidelines for its researchers, which encourage them to speak publicly about their areas of expertise — provided they do not stray too far into policy.

But that distinction can be difficult to draw and the resulting uncertainty, according to CSIRO's critics, has left scientists feeling frustrated and fearful.

A difficult decision

In March 2015, the Abbott government called for submissions on greenhouse gas reduction targets, ahead of the Paris climate summit in December.

But in an email on April 8, Jenny Baxter, then CSIRO's executive officer environment, told key managers and climate scientists the agency would not be making a submission.

She wrote:

"The questions posed in the discussion paper are very policy focused and difficult for CSIRO to answer directly as a trusted adviser. "CSIRO is already well connected into various relevant government agencies and processes and can likely achieve greater impact via these channels through targeted discussions and provision of information/advice."

Dr John Church, a senior CSIRO sea-level-rise expert who lost his job in a 2016 cull of the organisation's climate scientists, says he was "outraged" by the decision, since he believed the public had a right to hear from the scientists they funded.

He circulated Ms Baxter's email to colleagues with the opinion: "Disappointing, but hardly surprising that CSIRO has decided not to stand up for science."

Dr Church asked one particular colleague whether he was planning on "doing anything".

That colleague, a senior scientist in CSIRO's oceans and atmosphere division, replied saying he shared Dr Church's "disappointment" and believed CSIRO should not be operating "behind closed doors".

He also expressed concern CSIRO had already been "missing in action" at critical times, as far back as the lead-up to the 2009 Copenhagen climate summit.

Separate submission goes ahead

Top sea level rise expert, Dr John Church, lost his position at CSIRO during CSIRO's 2016 cull of climate scientists ( ABC News: Angela Ross )

Dr Church then decided he and several colleagues would make their own, private submission to the review.

He says he was "very strongly discouraged" by his superiors. Dr Church also says a series of private phone calls from management led to two junior colleagues withdrawing their names from the submission.

"I was willing to take the risk and see what happened; they had young families and couldn't take the risk," he says.

The submission eventually went ahead, without the names of those two junior authors, under the auspices of the Australian Academy of Science.

At the last moment, when it was clear he would not back down, Dr Church says CSIRO changed its position.

Senior management sent an email saying they were "happy" with his involvement in the Academy submission, and gave permission for his name to be listed "in the acknowledgements as a private individual".

My interpretation of that is they just didn't want to be caught out as trying to stop me," Dr Church says.

"Once they failed, they thought they had better be seen to be supportive."

CSIRO, however, argues it was simply ensuring the rules were followed.

"Originally, three scientists intended to make a submission in a private capacity," Mr Morgan says, adding that those original submissions would have breached relevant guidelines.

"This was discussed with the individuals concerned. Subsequent decisions to participate or not were taken by the individuals involved."

Fearless advice and trusted advisers

Mr Morgan also refutes the idea CSIRO was "missing in action", including in 2009.

"CSIRO officers provided evidence-based input … through relevant departments and were involved in many formal and informal discussions and briefings, media articles and public debates."

Nonetheless, repeated disagreements between scientists and senior management over the agency's role in communicating climate science point to fundamental divisions within CSIRO.

"When I joined the organisation they were known for giving fearless advice," says Dr Church, now at the University of New South Wales.

"Now, CSIRO likes to think of themselves as a 'trusted adviser' … there's an element of them being trusted to say what the government wants to hear."

Dr Church's colleague at the University of Melbourne, climate scientist David Karoly, says CSIRO management has tended to take "a risk-avoidance approach".

"They don't want to risk being perceived as providing government with advice that is inconsistent with government policy," he says.

Dr Karoly and others say this approach is fuelled by a fear of losing government funding.

Long-running difficulties

Accusations of political influence on communication of CSIRO climate research stretch back more than a decade, spanning the tenure of both Coalition and Labor governments.

In 2009, with Labor struggling to get its carbon trading legislation through the Senate, a CSIRO researcher claimed the organisation had tried to stop him publishing a paper that was critical of emissions trading.

"Managers said it was a political hot potato — too political to publish," says author of the paper Dr Clive Spash, a social scientist who was then part of CSIRO's Sustainable Ecosystems division.

Dr Spash, now chairman of public policy and governance at the Vienna University of Economics and Business, says he was harassed, became stressed, and resigned after he was refused the right to publish the paper in the journal New Political Economy, even as a private individual.

At last week's March for Science many expressed frustration that policy makers were not listening to scientists ( ABC News: Jonathan Webb )

As reported by Nature, an editor of the journal wrote to then science minister Kim Carr, accusing CSIRO of abusing the peer review process by requesting "major changes in the central arguments of the paper". Senator Carr has denied receiving that letter.

And much like Dr Church in 2015, Professor Spash says a junior co-author withdrew from this 2009 publication out of fear for their job.

"They bully and harass scientists to make scientists self-censor," Dr Spash says.

Another five years earlier, this time under the Howard government, then chief of CSIRO's climate change division Dr Graeme Pearman was reportedly forced out the door. Dr Pearman says this was because he spoke out about the need for strong CO2 reduction targets and carbon trading — a view that did not accord with Coalition policy.

"The real problem was that the message of climate change itself was being rejected," Dr Pearman says. "It was inconsistent with the worldview here in Australia. We were a resource nation, making significant incomes from the selling of coal and gas; we didn't want to see that world shaken."

In a 2006 Four Corners program on ABC TV, Dr Pearman was one of three scientists who claimed CSIRO had tried to gag them. The program linked these attempts at censorship with the political influence of the resources industry.

CSIRO's view, then as now, was that researchers should not involve themselves in policy advocacy.

When Four Corners asked CSIRO executive Dr Steve Morton about attempts to block Dr Pearman, the response was: "He's very free to talk about options for reducing greenhouse gas emissions, that's exactly what we're encouraging our staff to do.

"When it comes to being specific about which proportion of reduction by which date, that is clearly a policy prescription and that clearly intrudes upon the role of government."

Read our explainer about CSIRO's rules for researchers on the frontline.

Read CSIRO's full response to our questions.