The Northern Territory Environment Protection Authority's (EPA) recommendation that Glencore should be allowed to expand its McArthur River zinc and lead mine in the Gulf of Carpentaria has infuriated Indigenous and green groups.

Key points: Glencore should be allowed to expand its McArthur River Mine, the EPA has recommended

Glencore should be allowed to expand its McArthur River Mine, the EPA has recommended The NT and Federal Governments can decide whether to accept or reject the EPA's advice

The NT and Federal Governments can decide whether to accept or reject the EPA's advice The mine has contaminated fish with lead for six years

The EPA has advised the Territory and Federal Governments that it thinks the controversial mine "can be managed to avoid unacceptable environmental impacts and risks".

EPA chairman Paul Vogel said there would be a better prospect of protecting the environment if the company remained, rather than if the site was abandoned.

"We do not underestimate the significance of the potential impacts into the future," Mr Vogel said.

"But we believe that by keeping the company there, that has the skills and the resources and the capability to do the tests and monitor and review, we believe there's a much better prospect of delivering good environmental outcomes than just abandoning the site now."

In 2014, the ABC revealed Glencore's massive waste rock dump had started self combusting because it had mis-classified the amount of pyritic and reactive rock it was mining out.

The same year, the ABC also forced the company to admit that it had contaminated fish in McArthur River tributaries.

Since then lead in fish from Barney and Surprise Creeks have continued to breach Australian food safety standards.

The company has also breached its discharge responsibilities, with monitoring at its SW11 site returning readings of sulphate above allowable levels since 2013.

Glencore is still investigating how to stop the waste rock dump smouldering. ( ABC News: Jane Bardon )

'Not significant contamination': EPA

It has worried Indigenous residents in Borroloola, who have been warned since 2016 to limit their intake of fish.

"No-one don't fish in that river any more, no one don't swim in that river any more," Indigenous resident Gadrian Hoosan said.

But Dr Vogel said the EPA "would assert that there is not significant contamination of the McArthur River presently".

The EPA has recommended the company should be allowed to expand the mine and add another half a billion tonnes of reactive waste rock to the dump.

That includes pyritic iron sulphide rock which spontaneously burns on contact with air or rainwater, acid and salt-leaching rock, and rock which leaches heavy metals.

"Its a very disappointing decision and we think it epitomises why the Territory community doesn't trust our regulatory system," Lauren Mellor from the Minerals Policy Institute environmental group said.

In its environmental impact statement application in March last year, Glencore proposed leaving the waste dump on the river bank forever.

It proposed putting some of the most reactive waste rock from the dump and the tailings dam into the pit at the end of mining, and then allowing the pit the flood and reconnect to the diverted McArthur River.

Lauren Mellor says the EPA has potentially deferred problems for future generations. ( ABC News: Jane Bardon )

Call to backfill waste into pit

Indigenous residents and green groups have called on the Territory and Federal Governments to instead require the company to undertake the more expensive option of backfilling all of the waste into the pit, away from the McArthur River.

The EPA thinks the decision on what happens to the waste and how that is paid for should be deferred.

"The whole issue of backfilling absolutely still needs to be evaluated, within a proper process, with experts," Dr Vogel said.

Glencore has not yet found a way to stop the dump burning altogether.

Up to now, it has been trying to pack it more tightly and smother it with clay.

It is now proposing trialling different covers.

"It's not exactly like a fabric, but its built in sheets and you put it down, it's like very thick HDE plastic," mine general manager Sam Strohmayr said.

"If it smokes after all that then that has failed. So the trials will determine what is the best cover over time," Mr Vogel said.

The EPA thinks it would be better to allow the company to keep mining and expanding the dump and tailings dams, rather than risk it walking away.

"That really kicks the can down the road and makes McArthur River Mine the problem of future generations and future governments," Ms Mellor said.

The Territory and Federal Governments can decide to either take or reject the EPA's advice.

Glencore is asking them to consider the future of 800 mostly fly-in-fly-out jobs on the site.

The company has not yet gained permission from the Aboriginal Areas Protection Authority to raise the dump from the current 80 metres high to 140 metres, parallel with a sacred site on a nearby rock outcrop ridge, the Barramundi Dreaming.

The Authority is currently considering the objections of some the mine site's traditional owners.

The NLC's Joe Morrison said the report represents "an unacceptable approach".

'Unacceptable approach to environmental risk'

The Northern Land Council has condemned the EPA's advice.

"The sorry history of frequent environmental incidents at the mine and poor regulation mean that both the operator and regulator cannot be trusted," NLC chief executive Joe Morrison said.

"The report represents an unacceptable approach to environmental risk.

"It is merely hoping against hope and goes against the weight of evidence presented to the EPA.

"Further, the EPA report does not provide any confidence that the closure plan will not result in unacceptable environmental outcomes."

Mr Morrison accused the EPA of ignoring the "best practice approach to environmental management based on detailed characterisation of risk and prevention".

"The recommendation for approval is based on a hope that over the next 20 years, while the volume of waste rock and tailings accumulates, some technological solution will prevail," he said.