The area runs alongside the Tuggeranong Parkway, is bordered by the Molonglo River and sits behind the arboretum. It is to become home to 27,000 people over 800 hectares, with land release scheduled to start in the next 12 months.

The Suburban Land Agency has applied for an exemption from having to do an environmental impact assessment, despite the presence of endangered and vulnerable plants and animals, including the pink-tailed worm lizard. The project also involves the relocation of two critical critical 132kV lines that supply power to large areas of Canberra, which is one of the triggers that usually forces an environmental assessment.

Prof Auty has now told the government that she does "not feel comfortable with the approach being undertaken".

"I am concerned that [matters of national environmental significance], in particular the pink-tailed worm-lizard, and potential ... habitats within the project area are being overlooked in the Molonglo Stage 3 development proposal," she said in a submission.

She said 36.7ha of habitat for the pink-tailed worm lizard was within the future urban area and the impact had not been entirely addressed. She questioned whether the extent of the lizard's habitat was clear and urged the government to consider updated work on the superb parrot.

The Greens' Caroline Le Couteur and the Conservation Council have also objected. Conservation Council ACT director Larry O'Loughlin said there was no management plan for the Molonglo River reserve, and the government was yet to comply with a federal requirement for a buffer between the Kama nature reserve and housing.

The development traversed the habitat of pink-tailed worm lizard, and involved substantial clearing of native vegetation.

Ms Le Couteur said development did not meet the legal tests for an exemption. The Molonglo Valley was important not only for specific species, but for the movement of birds and other wildlife from the Belconnen hills to Mount Stromlo and the Murrumbidgee River, she said.

Caroline Wenger, convenor of the Umbagong Landcare Group at Ginninderra Creek in Belconnen, said it was concerning that the government would seek an exemption for such a major project.

The area was highly sensitive, used by endangered or declining species, and the proposal also involved cutting down all the pine trees around the arboretum, used by yellow-tailed black cockatoos. Most black cockatoo species were endangered and it might only be a matter of time before the yellow-tailed cockatoo joined them.

The land was steep down to the Molonglo River, and housing development could result in erosion from people walking down to the river and run off from hard surfaces, she said, asking whether the river would become "a glorified stormwater drain for the new development, as has been the case for Ginninderra Creek".

Gungahlin development had seen regular pulses of turbid water through through Umbagong at Macgregor as a result of inadequate sediment traps and it had been many years since she had seen a native water rat in the area, Dr Wenger said.

"Such close proximity to the river also means rubbish, nutrient pollution, invasives, domestic animals will be a problem. These are all issues we have at Umbagong. It is a pity that decision makers seem unable to prevent history from repeating itself.

"River corridors are prime wildlife habitat and are not only used by riparian species. Protected river catchments results in clean water for human populations. It should be a priority to protect them from unbridled development."

The Suburban Land Agency argues that sufficient environmental work has been done, so the impacts are well known without the need for a formal assessment.