Glencore has been given the green light to start work on its plans to vastly extend its controversial mining operations at McArthur River in the Northern Territory.

The resource company, McArthur River Mine (MRM), has sought to extend its mining operation until 2048, which will add on a further 1,000 years of rehabilitation and monitoring.

The mine, 1,000km from Darwin, has a potted history, with multiple allegations and instances of contamination of surrounding environment and mismanagement of toxic waste.

In December 2017, Guardian Australia revealed the company had accidentally dumped 63 truckloads of toxic waste near the river the previous year. The incident and the government’s investigation – which produced no report – were kept out of the public eye.

Guardian Australia has sought further information about the investigation through freedom of information laws, but almost two years later later is yet to receive any documents, for reasons that include objections from MRM.

In 2013, the suburb-sized waste rock pile combusted, and the resulting fire burned for more than a year, sending toxic smoke into the atmosphere. The incident prompted the NT’s environment protection authority [NTEPA] to demand MRM redo its environmental impact statement if it wanted to extend its operation.

On Tuesday, the NT minister for primary industry and resources, Paul Kirby, announced he had granted approval for an amendment to MRM’s mine management plan, “creating a pathway for the implementation of all 30 recommendations made by the [NTEPA]”.

The approval means that “under strict regulatory conditions” MRM can now start work on its overburden management project.

“Ongoing development of the mining industry in the Northern Territory is important,” Kirby said. “Our government expects it to be done in a sustainable and responsible manner, maximising economic benefits while focusing on minimising environmental impact.”

The NT’s approval followed federal approval from the commonwealth in June, a decision that came with a 3019 expiry date and which was not made public until revealed by BuzzFeed last week.

The amended plan also increases the company’s security bond, from $487m to almost $520m, which Gavin Mudd, associate professor at RMIT and chairman of the Mineral Policies Institute, described as “paltry”, given far less complex projects of similar scale required around $1bn.

Mudd said there were welcome aspects to the amendments, including the unprecedented stipulation that the mine’s environmental management plans must be made public, and three-yearly enforced reviews of monitoring policies.

However, parts of it were contradictory, he said, noting dual requirements that the health of McArthur River be protected from mine related impacts along its whole length at all times, and that its water quality “show improving trends” within 20 years of the cessation of mining.

“If you’re protecting the health of McArthur River there shouldn’t be anything getting out of the mine anyway,” he said.

He said the river quality should be tested against a benchmark of being a pristine environment, not “as an already impacted river”.

The chief executive of the Northern Land Council, Marion Scrymgour, said the approval was the latest example of traditional owners and Aboriginal people who lived in and around Borroloola being ignored.

“Aboriginal people in the mine area have consistently been denied involvement in decision making related to the mine, and have not seen the economic benefits that a native title mining agreement would justly bestow,” she said.

The approval also raised questions around the required establishment of an independent review panel, the set-up of which the mine will “assist” and fund.

Mudd said there were at least six critical areas of importance that required specific expertise on the panel for it to be properly monitored.

“The underlying subtext is it’s a problematic site with underlying issues and we need a good panel of experts to independently review everything.”

He said Glencore and the NT government would do well to have community-nominated experts on the panel, in part as recognition of their loss of social licence for the mine over previous years.

The NT government’s decision puts pressure on the Aboriginal Areas Protection Authority, the only remaining procedural roadblock for MRM.

The AAPA has not yet granted a certificate to MRM allowing it to almost double the height of its waste rock pile. The height is currently restricted to go no higher than 80m – the height of nearby Mount Stubbs, a Barramundi Dreaming site for local clans.

MRM has said it has an agreement with traditional custodians to increase the height but its validity has been disputed by some traditional owners and local people. Accidentally published government briefings in 2017 also cast doubt on it.

The NLC’s Scrymgour said the NT government’s decision was “premature”.

“Minister Kirby knows that an Aboriginal Areas Protection Authority certificate has not been obtained for the expansion of the Northern Overburden Encapsulation Facility and yet he has approved it anyhow,” she said.