It has also ticked off a modification to an environment management plan (EMP) for Maddingley Brown Coal at Bacchus Marsh.

The amendment upgrades the containment facility’s proposed design, bringing it into line with other plans.

“It does not change the nature of the material to be contained but adds additional controls,” the EPA said in a statement.

The Maddingley plan, along with another at Hi Quality’s Bulla site in Melbourne’s northwest, was approved in early September and prompted community uproar.

Both sites have been nominated to accept soil contaminated with PFAS chemicals after being dug up by tunnel-boring machines.

The three sites still need a green light from the Victorian government, with the joint venture running the tunnel project then able to choose the eventual dumping ground.

Tim Eaton, the EPA’s executive director of regulatory standards, assessments and permissioning, said the health of local communities and the environment was their “first priority”.

“Each of the EMPs has been rigorously reviewed and approved on the basis they meet strict conditions designed to protect human health and the environment,” Mr Eaton said in a statement on Monday.

“EPA will monitor any selected site closely to ensure it operates in accordance with its EMP.'”

Already delayed over the contaminated soil dispute, the $6.7 billion project’s builders have pushed to rip up their contract, sending a legal dispute to arbitration.

Toll giant Transurban took CPB Contractors and John Holland to Victoria’s Supreme Court after the builders asked to be let off their end of the bargain.

At least 200 workers on the project have lost their jobs since January because of the delays. The project is due to be finished in 2023, a year behind schedule.