Mining giant Glencore and the NT Health Department did not act on a recommendation from the Chief Health Officer to warn people living near the McArthur River Mine to not eat fish from three locations, Northern Territory Government documents show.

For more than a year Borroloola's Indigenous clans have worried reactive waste rock on McArthur River Mine and leaking tailings dams could be health risks and have been asking the Giles Government to tell them whether it is safe to eat fish from nearby waterways.

The mine in the remote Roper River region south of Arnhem Land on the Gulf of Carpentaria is one of the world's largest producers of lead, zinc and silver.

Mines department briefing documents released under freedom of information laws to the Environmental Defenders Office (EDO) showed the NT's Chief Health Officer recommended signs be erected warning people not to eat fish from Surprise Creek or Bing Bong Port, because of heavy metals in fish, oysters and mussels.

The briefing was prepared by the then mines department chief executive Scott Perkins for then mines minister Willem Westra Van Holthe and Chief Minister Adam Giles, in advance of a meeting in February with chief operating officer for Glencore's zinc assets, Greg Ashe, and the general manager of the McArthur River Mine, Sam Strohmayr.

The briefing said:

The Chief Health Officer and the Department of Health have an overall responsibility to safeguard the health of the public and requested that the Department of Mines issue an instruction to McArthur River Mining to erect signage along Barney Creek, Surprise Creek and within the immediate region of the Bing Bong Port advising people not to eat fish or other species from these waters because it may pose a risk to public health.

The briefing note said the miner had not put up the signs.

When the ABC inquired in May this year what warnings the health department had issued, it said it had warned adults to limit fish intake to three times a week, and children to twice a week.

The Environmental Defender's Office said it was "extraordinary" the mine was still operational.

"What we've known for some time, that these documents crystalise even further is just the systemic non-compliance with environmental and health regulation at McArthur River Mine," said David Morris, the EDO NT principal lawyer who is representing the area's indigenous clans.

"The Government's failure to come down hard on them when faced with that wilful disregard is quite extraordinary."

Fish with elevated lead level found in one creek: Glencore

In a statement, Glencore said that since October 2014 it had made significant improvements related to the management and treatment of waste rock, its tailings storage facility and improving water quality onsite, including flora and fauna.

The company said its fish testing in 2014 from the McArthur River and its tributaries found 10 from a sample of 347 fish had elevated lead concentrations.

Glencore said the elevated levels were only found in Barney Creek on the mine site.

"Testing of popular food fish upstream from Borroloola and near King Ash Bay did not indicate bioaccumulation of lead or other metals had occurred in these fish and hence are considered safe to eat," the statement said.

The failure of one of McArthur River Mine's tailings dams would have 'catastrophic consequences', government warned. ( ABC News: Jane Bardon )

Acid mine drainage plan 'deficient'

The briefing document also advised the Chief Minister that Glencore did not have to means to protect the environment from its McArthur River zinc mine.

It said Glencore's plan for managing the 88 per cent reactive waste rock it was mining out was "deficient" as the rock could cause acidic drainage.

The mines department rejected Glencore's mine management plan.

It said Glencore did not have enough clay and other non reactive material to encapsulate a waste rock in a dump, planned to cover 11km of land adjacent to the McArthur River.

The briefing advised:

The Department of Mines and Energy is aware that McArthur River Mining does not currently have a design to manage the material on the surface over the long term. Furthermore McArthur River Mining does not have access to sufficient clay and inert cover materials necessary to encapsulate the acid forming material.

The documents showed Glencore was asked to provide further information.

Mr Giles said on Tuesday what had been provided was still not sufficient.

Glencore said it was still operating under its mine management plan for 2012-2013 and that a proposed mine management plan it submitted for 2013-2015 was still under consideration by the mines department.

It said it was preparing an environmental impact statement on its waste rock.

The McArthur River Mine is the world's largest bulk zinc concentrate exporter. ( ABC News: Jane Bardon )

The company said its current work is considering the availability of benign material to contain potentially acid forming rock in the waste dump.

Another briefing prepared for the Chief Minister by the mines department chief executive in September 2014 said that McArthur River Mine was storing water laden with heavy metals in its Cell 2 tailings dam contrary to the conditions of its mining permit.

In June the dam was found to be leaking, indicating "a serious risk to the dam's structural integrity".

The department advised that a failure would have "catastrophic consequences" of "releasing highly toxic tailings into the McArthur River System".

The documents also said 300 cattle at risk of lead contamination from grazing near the processing plant were only picked up by a department inspector in June last year.

The Government tested five of the cattle and found one contained unsafe lead levels.

Glencore said it was working on a cattle management plan focusing on fencing in and around areas near the mining operation.

"All cattle within a 100 square kilometre radius were quarantined and were excluded from entering the local and export markets," the statement said.

"Animals that could not be mustered were destroyed onsite by Department of Primary Industries inspectors."

The department ordered testing of the cattle in June 2014.

Glencore would not say for how long cattle going to market had access to the mine site.

McArthur River Mining and its parent company Glencore were consulted about the contents of the documents before the Chief Minister's Department released them.

Chief Minister Adam Giles today said there was "no scientific link" to the lead detected in fish in the area and defended the Government's course of action.

"There's no scientific link to the mine in regards to this lead in fish and seafood out there, so I think that the advice that I'm given to date has been sufficiently advised."