Once again, mining giant Glencore has paid no royalties to the Northern Territory Government for its McArthur River Mine (MRM), a company report has revealed.

MRM, on the Gulf of Carpentaria, is one of the world's largest zinc deposits.

The mine has been plagued by problems since a waste rock fire in 2013 emitted toxic smoke, and there have been fears acid and metal drainage could contaminate fish in nearby waterways.

The company's report on its payments to governments for 2016 showed it paid "$0" in royalties to the NT Government that year.

It is the second report Glencore has released on its payments to governments; its first report, for 2015 payments, also showed the company also did not pay any royalties to the NT Government that year.

In a statement, Glencore said the NT's profits-based royalty regime allowed for capital investment offsets to be made.

"Over the past several years MRM has made significant capital investments including the Phase 3 Development project," the Glencore statement said.

NT only jurisdiction with profits-based royalty system

The Northern Territory is the only jurisdiction to have a purely profits-based mining royalty system, but the NT Government recently flagged it was considering changing it.

A report has revealed there were no royalties for the McArthur River Mine in 2015 ( ABC TV )

Treasurer Nicole Mansion said mining had made a significant contribution to the NT economy, but that it was time to look at the benefits of the Territory's profits-based royalty system.

"I think it's time we explore those options in discussion and in consultation with the mining sector," she said.

"It's important that we do have a discussion to make sure we have the right taxation regimes in place to ensure that we encourage investment in the Northern Territory and economic growth and create further jobs in the Northern Territory.

"But we do have to have some of these harder conversations, as well, to make sure that we have got the right systems in place to benefit the NT."

Experts say under profits-based royalty systems, royalty payments can fluctuate.

They also say that for profits-based systems to be effective, governments need to keep on top of auditing because the regime has a complex system of deductions, and working out the profits of large multi-national companies can be difficult.

In its statement, Glencore said it was audited annually by the NT Treasury against its operating agreements.

It also said over the past five years it had invested $2 billion into the Territory economy.

"We're proud of our contribution and the widespread value it brings — we provide direct employment for about 650 people and in 2016 spent more than $320 million on goods and services, much of which was sourced from local and regional businesses," the statement said.

Glencore declined to comment on the NT Government's possible changes to its royalty regime.

Glencore is arguing the economic benefits of the mine outweigh the environmental risks. ( ABC News: Jane Bardon )

Last royalty payment made in 2008

The Australia Institute think-tank this week issued a report on the future viability of the mine.

Both the NT and federal governments are considering the company's Environmental Impact Statement (EIS) application for the mine to keep producing zinc and lead for another 30 years.

"Based on the company's analysis, it's very unclear how you could come to a conclusion that the McArthur River Mine is even a net positive to the Northern Territory economy," report author Rod Campbell told the ABC.

Glencore estimates the mine will pay a total of $435 million in royalties to the NT Government over 1,000 years, but Mr Campbell said that was an unrealistic figure.

"The only known royalty payment of $13 million came in 2008 after a historic peak in the zinc price," the report said.

The EIS estimated Glencore would pay $1 billion in company tax to the Federal Government.

The Australia Institute assessed this as unlikely because, "it is known that the company often pays zero in company tax".

"ATO data shows that despite $108,107,933 in taxable income, Glencore entities paid no company tax in 2014-15," the report said.