Science Minister Greg Hunt insists an order to the CSIRO to focus on climate research came from the very top and reflects the focus of the new government.
The directive, which comes with $37 million over a decade and 15 new jobs, was jointly developed by Prime Minister Malcolm Turnbull and Mr Hunt, who both have "strong views" on climate science.
But it isn't expected to save scientists who have already lost their jobs.
Mr Hunt is refusing to admit chief executive Larry Marshall's decision earlier this year to cut climate change research had damaged the science body's reputation.
"This is a policy decision of the prime minister and myself," he told ABC radio on Thursday.
"We have laid down a position of a new government and new focus, a clear focus."
But the science minister says he is focused on strengthening the CSIRO's reputation.
"We are starting from where are," he said.
"Our job is to take where we are now and to strengthen the science and strengthen the reputation."
Dr Marshall initially said about 300 jobs would be replaced, but that was revised down after a public backlash and international criticism.
The CSIRO has embraced the new directive, Mr Hunt said.
The science minister insists Dr Marshall's job is still tenable, labelling him one of the outstanding science leaders in the world.
