The CSIRO aims to publish a controversial paper by one of its scientists attacking the federal government's climate change policies.
Dr Clive Spash claimed last week the science body was gagging him and the report, which rejects the government's proposed Carbon Pollution Reduction Scheme and suggests a direct tax on carbon.
The CSIRO does not allow its scientists to speak out on government policy as part of its charter.
But, faced with criticism that the organisation was silencing any opposition to the government, CSIRO chief executive Megan Clark sat down with Dr Spash to thrash out a deal.
They met in Melbourne on Monday to discuss how to get the paper, The Brave New World of Carbon Trading, out in the public arena.
But Dr Spash would need to amend it, Dr Clark said in a statement.
"I met with Dr Spash this morning to discuss a number of issues and in particular the paper and how it could be amended to comply with the CSIRO Charter," she said.
"We have agreed to resolve this matter quickly and all parties will now work to make the amendments with the intention to have the paper ready for publication."
They also decided that the paper must remain CSIRO-affiliated because it was created through Dr Spash's work at the organisation.
A CSIRO spokesman said the issue was due to be sorted by Friday at the latest.
Federal Minister for Innovation, Industry, Science and Research, Senator Kim Carr, rejected any suggestion that the report had been quashed, nor would it be rewritten before release.
However, Senator Carr stressed that reports written under the CSIRO banner had to be vetted by the organisation before they could be published.
"Management has got a responsibility to ensure that people who want to use the brand name do so properly," Senator Carr told AAP on Monday.
"People want to know what the CSIRO stands for - and it's not necessarily what Joe Blogs says."
Senator Carr said he had not seen the report and did not know what changes CSIRO management had suggested be made to it, but he had "no doubt whatsoever" that the report would be published.
"It's about making sure the authority and the integrity of the CSIRO is maintained," he said.
"We have no problem about the report being published - it's not an issue, it's not an issue.
"It is important, however, that people who work for the CSIRO do talk to their colleagues."
Senator Carr said the government was "not seeking to prevent people from having their say".
"We take the view that research is contestable, there is no finite answers.
"This is about people putting forward ideas for public debate.
"So we say to people: 'you are encouraged to put your name forward, but you also have to expect others will have a say about this'.
"They have a right to be wrong."