A growing waste rock pile over 100 metres high at Glencore's McArthur River Mine will come close to the culturally significant area, the NT Aboriginal Areas Protection Authority says.

"By our estimations, the work associated with the waste rock pile will come within 35 metres of the boundary of that site," chief executive Ben Scambary said on Tuesday.

"This year the scale of the mine expansion raises some quite serious questions about the ongoing maintenance and protection of sacred sites on the lease, and also access for custodians to those places into the future."

Speaking to a federal parliamentary inquiry into Rio Tinto's destruction of 46,000-year-old caves at Juukan Gorge in Western Australia, Dr Scambary said there were also concerns about an archaeological site at McArthur River where Indigenous stone tools had been found.

"It's a quarry site that's considered to be of moderate to the high significance within the bounds of the development," he said.

Dr Scambary said a request to salvage the tools from the mine - about 800km southeast of Darwin - had been made "but a decision hadn't been forthcoming".

There also questions about whether the 2004 authority certificate permitting work at the zinc, silver and lead mine - where native title has been extinguished until 2046 - covered the current expansion.

Dr Scambary said APPA would "need to be satisfied that there will be no impact of the sacred sites" before a certificate extension would be granted.

"It's been a very tense situation. The company asserts that it continued to undertake works at the mine presumably on the expansion in accordance with the existing certificates," he said.

"They've also lodged a ministerial review which is in play."

The McArthur River Mine has been dogged by environmental incidents and claims its continued operation could damage the sites.

Some of the problems identified include burning waste rock emitting sulphur dioxide plumes, which took more than six years to rectify with the NT mining regulator.

A seeping tailings dam also risks contaminating groundwater with metal and acid, according to a recent report from the University of NSW's Global Water Institute and the NT Environmental Centre.

Researchers also found that 22 Indigenous sacred sites were potentially under threat from the mining operations, including the Djirrinmini waterhole, which is believed to be a breeding site for critically endangered sawfish.

Traditional owners of the site - the Gudanji, Yanyuwa and Yanyuwa-Marra peoples - want compensation for alleged damage to the cultural sites and the loss of their native title rights.

They blame the NT government for penning the deal for the mine with Mount Isa Mines Ltd in 1992 and have lodged a case with the Federal Court.

Traditional owners have also recently launched legal action against the government in the NT Supreme Court after it slashed the mine's environmental security bond by almost $120 million to around $400 million.

Glencore said it would obtain the appropriate approvals from the AAPA for any future mining plans that may require amended or new authority certificates.

"We operate under stringent conditions set down through NT and federal legislation as well as conditions of Aboriginal Areas Protection Authority certificates, designed to protect Sacred Sites," it said in a statement.

Australian Associated Press