The Federal Government has granted emergency heritage protection to Melbourne's St Kilda Road in an attempt to stop the removal of 100 trees for the Metro Rail project.

Environment Minister Josh Frydenberg issued the protection order, which lasts for 12 months, while the National Heritage Trust decides whether to grant the boulevard a permanent listing.

The tree-lined strip of road leads out of the city and past the Shrine of Remembrance towards the south-eastern suburbs.

The $11 billion rail project will see a new nine-kilometre tunnel under the CBD and five new stations.

The Andrews Government has warned construction will cause major disruptions to the city.

About 100 trees will have to be removed from St Kilda Rd, but Mr Frydenberg said they needed protection.

"The St Kilda Road precinct is an iconic part of Melbourne, with its historically important 19th century boulevard," he said.

"It is associated with the Shrine of Remembrance, its ceremonial landscape and the design heritage associated with the Domain Parklands."

He said that when the Victorian Government first sought approval for the development it was given the all clear because the area was not protected.

"The decision to give the area emergency heritage protection cannot revoke this decision," he said.

"However, in seeking to protect this historic area, I have written to the Premier of Victoria asking him to reconsider the project design to lessen its impact upon the surrounding landscape, including the trees that give important character to the precinct."

Liberals 'playing politics' with infrastructure projects

The move angered Victoria's Minister for Public Transport Jacinta Allan, who told ABC Radio Melbourne it was a political stunt.

The trees will be removed to make way for a nine-kilometre train tunnel. ( ABC News: Giulio Saggin )

"It doesn't matter whether they are Victorian Liberals or Canberra-based Liberals, they are all about stopping this number one infrastructure project," she said.

"Preliminary advice is that the early works can continue, because the Federal Government has previously given us their approval for those early works," she said.

"What this can potentially impact is the major stage of the project."

The federal and state governments have not seen eye-to-eye when it comes to infrastructure projects in Victoria.

The Commonwealth had withheld $1.5 billion put aside for the previous government's East-West Link after the Andrews Government scrapped it.

It was later released as part of a different package, but Ms Allan slammed her Canberra counterparts for giving Victoria less than its fair share of funding.