Four Melbourne councils have launched a Supreme Court legal challenge to the Victorian Government's $16 billion North East Link project approval.

Manningham, Banyule, Whitehorse and Boroondara councils filed the challenge this week, arguing that the project assessment was invalid because the proposed reference design was just a “concept”.

The controversial project was approved by the State Government last year, singing off on two new 6-kilometre tunnels, major upgrades to the Eastern Freeway and Melbourne's first dedicated busway from Doncaster towards the city.

The councils say the reference design did not provide “any clarity in regards to what will actually be built”.

“Too much about the project has been left to be determined at a later time which excludes the community, affected stakeholders and councils from the process,” their statement claimed.

“This is not the way this process should work. It is critical that all decisions made in relation to this significant project are made with a clear understanding of what is proposed.

“By the time that a design is finalised, there will not be a proper opportunity for community members and councils to provide input and make submissions in relation to the potential impacts.”

Minister for Transport Infrastructure Jacinta Allen insist the project went through an “extensive” consultation process.

“It's been through an exhaustive independent planning process,” Ms Allen told the ABC.

“And it appears that these councils would rather choose to spend potentially millions of dollars of rate payers' funds to keep trucks on local roads and to not provide relief that would come in travel time savings that would be delivered through the North East Link.”

An independent advisory panel criticised the project in a report last year, saying it would do considerable damage to communities.