Traditional owners are calling on the Northern Territory government to not allow a fracking company to move from exploring the Beetaloo Basin to selling gas, after it failed to report a find of ancient Indigenous stone tools near one of its exploration wells to the territory's heritage regulator. 

Empire Energy is planning to move from exploration fracking to selling gas from its Carpentaria Pilot Project, situated 160 kilometres east of Borroloola, next year.

Under its project conditions, the company was required to check for Aboriginal cultural heritage sites to be avoided.

Karranjini traditional owner Cain O'Keefe said he had been excited to join Empire Energy surveys which found that its archaeologists determined was a "significant" "medium density archaeological site", containing stone tools, near its Carpentaria 4 exploration well named Balbirini 3.

"I found them – a stone axe head and other pieces [were] in lines in a few trees, and 100 metres from that, a few spearheads," Mr O'Keefe said.

"It was so emotional. It took them that long to make a stone head axe from hand – it was a nice piece you hold with either your left or right hand."

He is now angry Empire Energy has reported to the NT environment department it has breached its project conditions, by failing to notify the government's Heritage Branch that stone tools were found at Balbirini 3 in August 2022, until January this year.

Mr O'Keefe said he was also devastated Empire Energy has reported grind stones, a spearhead and scraper were moved from the site to another area – a rock shelter named Balbirini 2.

"I'm disappointed – it's disgraceful," Mr O'Keefe said.

"Someone left them there maybe 60,000 years ago, things can't be moved from where they're left."

Mr O'Keefe and other traditional owners, including Joni Wilson, have written to the Heritage Branch asking it to stop the gas expansion project, and to commission an independent archaeological survey of Empire's EP187 gas lease.

"It's heartbreaking that there's been cultural artefacts that [have] been moved," Ms Wilson said.

"They shouldn't be touched — all the Aboriginal people know that, and they haven't been touched for centuries until the mining company [came] to do exploration."

Empire Energy responded in a statement that it was "committed to genuine concern for cultural values" and the stone artefacts were moved to another site by some traditional owners "under their own initiative".

The Heritage Branch has told the ABC it is investigating.

However, Ms Wilson wants a wider NT government investigation of all the breaches Empire Energy has reported to the environment department during the project.

Over the past four years, they include spilling drilling mud, allowing wastewater storages to fill up too high, storing wastewater in dams and tanks with leaks and tears in linings, building gravel pits outside approved areas, and not checking for endangered Gouldian finches before land clearing.

"They said that none of this would happen, and it's happening, and we don't know what the solution is," Ms Wilson said.

Ian Wright, an associate professor of environmental science at Western Sydney University, said he thought the drill mud and wastewater breaches in particular could threaten the NT's environment.

"It's an enormous worry. The chemicals used for the hydraulic fracturing process, or even just the drilling muds, are hazardous to human health and also to the plants and animals in the environment as well," he said.

Empire Energy responded that "none of these issues resulted in material environmental harm," "no fluids were spilled from tanks" or dams and "no finches have been harmed".

In a statement, NT Environment Minister Kate Worden said the government was "doing its job of comprehensively assessing the matters raised".

The NT's Environment Protection Authority (EPA) last month decided the Empire Energy expansion project did not need a full environmental impact study because it "doesn't have the potential for significant impacts on the environment".

Ms Wilson said she felt the NT government's response was inadequate.

"The government needs to be more alert to Empire Energy and know what's going on on the country, they need to do more work on protecting it," she said.

"Because our home is this bush, and we want it for the next generation."