Political pressure resulted in a series of legal errors made by the Environment Protection Authority, Ombudsman Deborah Glass said in a scathing report following an investigation launched last year.

The EPA overlooked human rights concerns and failed to properly consult with local communities when deciding where tonnes of contaminated soil from the $10 billion tunnel project would be dumped, Ms Glass found.

Residents around three approved sites in Bacchus Marsh, Ravenhall and Bulla were "left in the dark", she said in her report tabled in state parliament on Tuesday.

Failure to provide appropriate information was unreasonable, Ms Glass said.

Construction on the tunnel project came to a halt in 2019 after Perfluoroalkyl and Polyfluoroalkyl substances (PFAS) were found in groundwater samples along the route.

Human rights issues were a focus for affected residents, worried about the impact of PFAS on themselves, their children, waterways and wildlife, Ms Glass reported.

"Such was the level of concern that two community groups started legal action in 2020 to challenge the EPA's decision," she said.

"The EPA was compelled to revoke its decisions, but then approved three fresh plans for the landfill operators in early 2021."

The environmental regulator also compromised its ability to act independently, Ms Glass said.

She found the EPA was under pressure to resume the project and assisted the Department of Environment, Land, Water and Planning in establishing regulations to enable potential sites to receive the spoil.

Opposition Leader Matthew Guy called the West Gate project a government failure.

"The government are the ones who manage the project. It's about time they took responsibility for their own failings," Mr Guy said.

"This project has massively blown over cost, now we find there's issues with toxic soil and the dumping of it."

The EPA has committed to improving its practices.

"We are focused on continuous improvement and growth in all aspects of our work," the regulator said.

The trouble-plagued project by Transurban, John Holland and CPB Contractors had been scheduled for completion in September this year, but the opening has been delayed for at least another three years.

The 4km road links the West Gate Freeway at Yarraville, in Melbourne's inner-west, with the Port of Melbourne and CityLink at Docklands.

Initially priced at about $5.5 billion the cost rose to $6.7 billion in the final proposal stage.

Last year Transurban announced a further increase to $10 billion prompting a stoush over who would foot the extra bill.

The state government initially contributed $2.7 billion but last year tipped in a further $1.9 billion after "complex" negotiations.

Australian Associated Press