Defence has put the cull on hold after it asked the ACT Government to approve a translocation trial for scientific purposes.

A report to the ACT Government, issued earlier this month, recommended the cull of about 400 kangaroos go ahead without delay to protect lowland native grasslands and threatened species. It also said relocating the kangaroos would be inhumane.

The push to defer culling at the Belconnen naval site has left the ACT Government in a "difficult situation" and was labelled "survival of the cutest" by the Opposition.

ACT Chief Minister Jon Stanhope said the Government was now in a "cleft stick" as a result of the Defence decision to defer the cull while a trial took place.

"All the expert advice the unanimous advice of all experts engaged by both the ACT and Commonwealth governments is that the cull should proceed. The Commonwealth has chosen not to adopt that position so it does leave the ACT Government in a difficult situation," he said.

Mr Stanhope acknowledged he had been deeply frustrated by the Commonwealth's vacillation but had accepted Defence's new position and was willing to work with it.

"If the only way I can achieve that outcome is for the ACT Government with whatever reluctance to agree to translocation then at the end of the day we achieve our ultimate outcome, which is to protect the grasslands," he said.

Mr Stanhope criticised Defence over the delays, saying it had known about the planned cull for five years.

He also dismissed reports the land had been earmarked for public housing.

"Absolutely not. The grasslands within the fenced areas at Lawson are high-quality native grasses."

ACT Commissioner for Sustainability and the Environment Maxine Cooper said that less than 1per cent of Australia's grasslands remained intact. "We're in a crisis situation," Dr Cooper told ABC Radio. "To do research now in the middle of a crisis is not a strategic approach at all."

The decision also raised questions about national kangaroo culling policies, she said.

More than 312million kangaroos are culled around the country each year.

Last week the air force shot and killed more than 700 wallabies on the Tindal RAAF Base, near Katherine, in the Northern Territory. RSPCA chief Michael Linke said the animal welfare group had provided Defence with questions and issues which it believed needed to be addressed, and he had left the meeting with no feelings one way or the other.

"We're happy with the information we were able to present.

" It's up to Defence now, they're going to put forward their own research.

"How Defence will manage their land is ultimately their decision. It's good to get a hearing."

Mr Linke said scientific trials could not be invented overnight and Defence's decision to try alternative kangaroo management strategies raised a number of questions.

"The RSPCA has maintained that irrespective of the outcome the welfare of all those species are the things that remain paramount to us."

Wildcare president Suzy Watson said the environmental experts engaged by the ACT and Commonwealth governments were not necessarily specialists in kangaroos.

"If we look at that expert panel it is important that we recognise actual experience with kangaroos on a regular basis," she said.

"One of the things that our group has is that actual experience. And we can categorically tell you that translocation is possible. One of the cases I can refer to has a 95 per cent success rate. That was in Queensland with 288 kangaroos. So it is possible and it can be done."

Ms Watson said translocation was not always the solution and other methods such as reproductive control might be considered.

"I think it's about coming to grips with the fact that in this day and age we have to come up with in these particular circumstances a solution."

Greens MLA Deb Foskey said she was deeply concerned that the politics of the kangaroo cull had overtaken good science and the difficult issues could not be shirked.

Dr Foskey also criticised the ACT Environment Commissioner's early report into the kangaroo issue, saying there had been a "paucity of information" behind the commissioner's dismissal of translocation.

"That lack of scientific rigour has come back to bite the ACT Government," she said.

Opposition environment spokeswoman Vicki Dunne said the Defence trial was a last-minute move and the endangered wildlife species at the Belconnen grasslands site were being ignored.

"They're transfixed by the notion of the survival of the cutest," she said.

"There is no one out there advocating for the survival of the perunga grasshopper and the mouthless moth."