Tearing up Swanston Street for at least two years to build the Melbourne Metro rail project would divide Melbourne worse than the Berlin Wall, Premier Denis Napthine says.

Dr Napthine on Monday confirmed reports that the state government was looking at alternative options for the Melbourne Metro rail tunnel. It had originally been planned to run from Kensington to Parkville, continue under Swanston Street with two CBD stations, then to the Domain Interchange and join at South Yarra station.

The Premier said the government was still committed to building a rail project to increase capacity on the state's passenger and freight rail networks.

"We have a lot of options on the table, the original Metro rail capacity project had raised some challenges, particularly the proposal in that project of having Swanston Street closed for two years plus, and completely dug up," he said.