Western Australia’s government could have the power to approve activities that could make a threatened species extinct, under biodiversity laws now before state parliament.

The provision has been dubbed “the God clause” by scientists and conservationists, who say giving the environment minister discretion to effectively authorise the extinction of a species contradicts the very purpose of biodiversity legislation.

It is part of the biodiversity conservation bill 2015, introduced by the Barnett government as an update to the 66-year-old Wildlife Conservation Act.

Under that legislation, the environment minister may authorise a person, corporation or government authority to “take or disturb” a threatened species. If the taking or disturbance “could be expected to result in the threatened species becoming eligible for listing as an extinct species in the near future”, the minister must also get the approval of the state governor.

The state opposition voted against the legislation in the WA lower house last week but it passed without their support. It is due to be debated in the upper house in August, where the Greens have said they’ll support Labor in opposing the bill unless significant amendments are made.

Labor’s refusal to support the laws came after the Environmental Defender’s Office called them “illusory at best”.

The environment minister, Albert Jacob, said Labor’s decision not to back the proposal was “irresponsible and short-sighted”, saying the legislation “has the right key features sought by most of the community”.

It does not have the features sought by the scientific community, which is calling for an independent advisory committee on threatened species, similar to the threatened species committee included in the federal Environment Protection and Biodiversity Conservation Act.

Emeritus professor of environmental science at Murdoch University, John Bailey, said the legislation in its current form had the potential to hasten the extinction of WA’s critically endangered species.

“Biodiversity legislation is passed to preserve wildlife and it would be odd to have a provision that has an opposite effect,” he said. “The only check and balance is that the minister needs to inform parliament when he’s exercised this particular power, and our concern is that would be after the fact.”

Bailey was the chair of the state-run Conservation Commission for nine years and is considered an authority on wildlife conservation in WA. He has joined 12 other scientists, including Prof Fiona Stanley, to form the Leeuwin Group to lobby against the legislation

He told Guardian Australia the broad ministerial discretion in the legislation would give developers and governments an “easy out” for approving projects that could otherwise have been challenged in court.

It would also allow the minister to decide what species are most worth protecting, which meant high-profile critically endangered species, including numbats, were probably safe, while less well-known species, like subterranean fauna (fish, invertebrates), may not be. WA has 4,000 species of subterranean fauna, most of which are endemic and 40 of which are listed as threatened.

“We think that the ‘God clause’ was put in there for species like the subterranean fauna,” Jenita Enevoldsen, WA director of the Wilderness Society, told Guardian Australia. “Some of those subterranean fauna have stopped mines going ahead, but they are unique species.

“We don’t think it should be up to a minister to allow the destruction of a species.”

Enevoldsen said the legislation did introduce some positive changes, like increasing the penalty for taking an animal from a threatened species to $500,000 and codifying threatened species recovery plans, but counteracted that by introducing other changes such as excluding fish and shellfish from the definition of fauna.

The penalty for catching a critically endangered sawfish from the Fitzroy river was only $10,000, 50 times less than the penalty for killing a dolphin.

The legislation also provides broad exemptions for activities that could indirectly cause the destruction of the species, such as land clearing, logging or increased carbon emissions.

“So it’s illegal to go and kill a numbat but it’s perfectly legal to go and bulldoze the habitat of the numbat, or burn it, or destroy it by other means, and, in the process, kill the numbat,” Piers Verstegen, director of the Conservation Council of WA, told Guardian Australia.

“But pretty much the majority of threatening processes do not occur when people go and deliberately kill native wildlife … most of it’s indirect.

“If it doesn’t address any of those most serious threats then it’s not worth much as a piece of biodiversity legislation.”