The Climate Change Authority is hanging in limbo as it waits to see if the Federal Parliament will pass legislation to axe it.
But its chairman, Bernie Fraser, has declared the "damage has already been done" and that uncertainty about its future had caused almost half of its staff to quit.
Mr Fraser, a former Reserve Bank governor, told a Senate estimates hearing on Tuesday that even if the Parliament did not abolish the authority, as per the Abbott government's wishes, he did not know how its work could go on with just 20 staff members left.
Legislation to scrap the authority has been defeated once by the Parliament but its funding has ceased in the federal budget.
"We don't know what's going to happen to us," Mr Fraser said.
"But in a sense, the damage has already been done as far as the Climate Change Authority is concerned.
"We started off with a capable, professional team of 36 people.
"We're now down to 20."
The hearing was told that 16 staff members had quit because of the uncertainty, rather than taking voluntary redundancies.
Mr Fraser remarked that nobody wanted "to hang around under such a cloud".
Parliamentary secretary to the Environment Minister Simon Birmingham told the hearing it was "regrettable" the Parliament had not passed legislation to axe the agency the first time around.
The comments came after a tense estimates hearing overnight where the government was unable to produce modelling to show how much of its 5 per cent emissions reduction target it expected to reach with its Direct Action policy.
Officials told the hearing it was "premature" to be specific about what cuts would be achieved as elements of the policy, including safeguard mechanisms, were still under design.
Senator Birmingham said a "concrete pathway" was difficult as projections on emissions were updated on a yearly basis, but the government was committed to 5 per cent.
Greens senator Scott Ludlam responded that he would "be happy with a rough guess".
"I think [Environment Minister Greg] Hunt has used the word 'confident' quite a bit," he said.
"If you don't have those numbers on what basis does the Minister go out every day claiming how confident he is if you haven't even designed the policy yet in the middle of 2014?"