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The construction site of the hydroelectric facility at Muskrat Falls, Newfoundland and Labrador is seen on Tuesday, July 14, 2015.Andrew Vaughan/The Canadian Press

Work is set to resume at the Muskrat Falls hydroelectric site after the Newfoundland and Labrador government reached a deal with indigenous leaders that will add more delays to the controversial megaproject.

Provincially owned Nalcor Energy used buses to remove protesters who had stormed the site last week and was bringing back about 1,000 employees to complete the work needed to protect the site's infrastructure over the winter.

Under the agreement, leaders from three indigenous communities will review engineering reports with the assistance of outside experts in order to be satisfied with Nalcor's rationale to begin partial flooding. The utility says it needs higher water levels to protect the site from ice damage.

Assuming that step is taken, the government has ordered Nalcor to then lower the water level in the spring to assess whether it should clear away more vegetation and topsoil to reduce the release of methylmercury into the food chain. The extent of any clearing work is still to be determined, but it clearly would drive up costs and add to delays that have already plagued the project.

In a statement on Wednesday, Nalcor's chief executive officer, Stan Marshall, said the company welcomed news of the agreement and would comply with its terms.

"Our immediate priority is to resume normal operations at site in order to ensure completion of critical work to protect the site infrastructure for winter and to allow winter operations," Mr. Marshall said.

"We are assessing the financial and schedule impact of the new agreement, which cannot be determined at this time."

Premier Dwight Ball met late into the night on Tuesday with leaders from the Innu Nation, the Nunatsiavut government and the NunatuKavut Community Council to address their concerns that the release of mercury from the project would contaminate their traditional food sources, including fish and seals.

The project is already behind schedule and over budget. Estimated costs have soared to $11.4-billion from $7.4-billion four years ago and first power has been delayed from 2017 until 2019.

Mr. Marshall was appointed to replace long-time Nalcor CEO Ed Martin earlier this year and ordered a reassessment of the project before concluding that there had been too much work done and money spent to cancel it, even though the cost had ballooned to $11.4-billion from $7.3-billion.

Nalcor's partner, Halifax-based Emera Inc., has continued work on the undersea transmission links that would bring power from Labrador to Newfoundland, and from the island to Nova Scotia.

Emera owns 60 per cent of the Labrador link and 100 per cent of the one to Nova Scotia, and will take 20 per cent of the power from the 824-megawatt hydro project.