Melbourne's iconic St Kilda Road has been permanently added to the National Heritage List, in a move coming too late to stop trees being removed for the Metro Tunnel project.

Emergency heritage protection was granted by the Federal Environment Minister Josh Frydenberg a year ago, in an attempt to prevent the loss of about 100 trees.

Two nine-kilometre tunnels will be bored along the busy thoroughfare to link the inner city suburbs of South Yarra and South Kensington at a cost of $11 billion.

Victoria's Public Transport Minister Jacinta Allan labelled national heritage listing a political stunt aimed at stopping the project from going ahead.

The listing covers more than 100 hectares of land including St Kilda Road from the city to St Kilda Junction, the Shrine of Remembrance, Melbourne Observatory, Government House and Kings Domain.

The precinct will be known as Melbourne's Domain Parkland and Memorial Precinct.

In making the announcement, Environment Minister Frydenberg conceded permanent listing could not overturn the earlier decision to remove the trees.

Ms Allan said eventually the number of trees along St Kilda Rd would double. ( ABC News: Kathy Lord )

"It's very disappointing that the Andrews Government has destroyed those trees on St Kilda Road," he said.

"I looked at every particular angle that was available to us to try and reverse that decision but unfortunately at the federal level we didn't have the authority to do so."

"[However] it's terrific news that Melbourne's Domain Parkland and Memorial Precinct will now be protected.

"This is testimony to the important cultural, historic, environmental and Indigenous values that these sites represent."

St Kilda Rd and the surrounding precinct developed over the course of the 19th century and became the place to commemorate significant events such as annual Anzac Day parade.

Ms Allan said the number of trees along St Kilda Road would eventually double.

"Care has been taken to minimise the impact as much as possible." Ms Allan said.

"For every one tree that's being removed in this area, two trees will be replanted."

St Kilda Road and the surrounding area joins the Sydney Harbour Bridge, Uluru and the MCG on the National Heritage List.