Environmentalists have slammed the Northern Territory government for handing a gas company partial approval to begin fracking-related works in the Beetaloo Basin, saying the decision was made in “unusual” circumstances and without proper consideration of the impact on local species.

Empire Energy, a firm with links to the Liberal party, has been the focus of Senate scrutiny since it was awarded $21m from a $50m federal grant scheme to explore the Beetaloo Basin as part of the Coalition’s gas-led economic recovery.

The federal resources minister, Keith Pitt, awarded the grants in July, despite the company lacking the environmental approvals from the NT government that it needs to drill in the basin. The commonwealth’s grant scheme only requires that companies begin the approval process.

Late last week, the NT government uploaded a “partial” approval of the company’s environmental management plan. The partial approval will allow it to proceed with civil works and land clearing, while a final decision to approve drilling and fracking is pending.

The approval appears to have been given 10 days ago, but only publicly emerged on Monday.

The Protect Country Alliance – a network of landholder, community and civil society groups concerned about fracking in the NT – criticised the manner in which the partial approval was granted.

Graeme Sawyer, an alliance spokesperson, said it was a “way of letting fracking companies push ahead before fully assessing the impacts and risks of drilling and fracking several gas wells”.

Sawyer said the approval ignored new information from preliminary research through a strategic regional environmental and baseline assessment (SREBA), which revealed the presence of endangered species and new species in the area. That assessment has not been completed.

“The entire purpose of the SREBA was to research what species may be present in this little-explored part of the territory – this hasn’t happened – so there’s no telling what undiscovered and endangered animals may disappear thanks to this fracking project before we even know they’re present,” he said.

“The [Michael] Gunner government is ignoring science just to push through an unwanted fracking project that puts groundwater, communities, and the environment at risk.”

The Environment Centre NT also criticised the “unusual” decision. The ECNT was particularly alarmed at the involvement of the territory’s Department of Industry, Trade and Tourism in the process.

In 2018, the Pepper inquiry into fracking in the NT recommended the industry department should have no role in regulating the sector because of its competing role in promoting it.

In this case, the department provided advice to the minister on the environment management plan and will do so again for the gas well operation management plan, a key document that ensures well integrity and helps prevent contamination.

“The Pepper inquiry said really clearly … we can no longer have the department responsible for promoting the industry in charge of regulating the industry,” ECNT co-director Kirsty Howey told the Guardian.

“So a centrepiece on the entire regulatory regime that we were all pinning our hopes on was that all approvals were handled by the environment minister and environment department. Instead of doing that, they’ve created this strange hybrid system.”

NT government defends process

The NT environment minister, Eva Lawler, rejected any suggestion the process was unusual.

A spokesperson said the minister had taken advice from petroleum engineers in the industry department about the environmental management plan. This was entirely appropriate, the spokesperson said.

The minister is yet to make any decision about approving the environmental management plan for the drilling and hydraulic fracturing activities.

“The minister for environment has not yet received technical advice from the petroleum engineers to inform her decision about the part of the EMP that relates to drilling and hydraulic fracturing,” the spokesperson said. “The minister will make a decision on that part of the plan in due course.”

The approval is also conditional on further research being conducted on land clearing and the potential impact on a species of endangered finch.

The grants to Empire have been put under scrutiny on two fronts: through a federal court case brought by the ECNT and the Environmental Defenders Office arguing the minister didn’t properly consider climate impacts in approving the expenditure; and through a Senate inquiry that has focussed on Empire’s political connections.

Empire has donated to both sides of NT politics and is chaired by Paul Espie, a frequent Liberal donor, the inquiry has heard.

In the months prior to the announcement of the grants scheme, the company paid for a charter flight for the federal energy minister Angus Taylor and the head of a Liberal party fundraising forum, taking them to inspect a well site in the Beetaloo, the inquiry heard. The company denies it was attempting to lobby Taylor.

The inquiry was also provided with email records that show Empire had asked Taylor’s office for information on the grant scheme’s “eligibility criteria” and the “application process” well before the program guidelines were released.

The company has denied its connections or donations have played any role whatsoever in the grant process and says it followed “due and proper process at all times”.

Taylor was not the minister responsible for the grants and the money was awarded by a three-member panel that found the company met the relevant eligibility criteria.

In a statement to the ASX on Friday, Empire said the civil works would begin in the coming days. “Approval for the drilling and fracture stimulation components of the EMP are expected in the coming weeks.”

Empire told the Guardian it would not undertake any work without the proper environmental approvals in place. A spokesperson said it went to “great lengths” to ensure it had a minimal environmental impact.

“The Environment Management Plans we have submitted include extensive ecological surveys,” the company said. “The highest environmental and safety standards and respectful engagement with local communities and traditional owners are core to Empire’s values and business strategy.”