The proposed Melbourne Metro rail tunnel will still deliver passengers into the city centre, despite the Napthine government's recent decision to scrap plans to tunnel beneath Swanston Street.

It was revealed this week that the government is considering realigning the $9-11 billion rail tunnel so that it runs through Fishermans Bend south-west of the CBD, radically rewriting the script for Victoria's biggest public transport project.

Melbourne's lord mayor Robert Doyle said shifting Melbourne Metro west would be a "100-year catastrophe for the city" and urged the state government to recommit to the route that was originally proposed.

"The Berlin Wall was a 30-year mistake but not building Metro One in the original way it was designed would be a 100-year catastrophe for our city," Cr Doyle told Jon Faine on 774 ABC on Wednesday.

"We need that underground station [in Parkville] as part of Metro One right in the heart of where our new cancer centre will be, our research precinct, the University of Melbourne, the Royal Melbourne Hospital, the Royal Women's Hospital, it's just crucial that we service that with a large underground rail station," he said.