St Kilda Road and a surrounding precinct encompassing the Shrine of Remembrance and Domain Parklands have officially joined the Sydney Harbour Bridge, Uluru and the MCG on the National Heritage List.

But the decision – announced by federal Environment Minister Josh Frydenberg on Sunday – comes too late to save nearly 100 plane and elm trees from the chainsaw.

Josh Frydenberg with Dr Lyndon Ormond-Parker (left) and Dean Lee (middle) in front of the Shrine of Remembrance. Photo: Chris Hopkins

The Melbourne Metro Rail Authority plans to chop down 95 trees along St Kilda Road to build the Andrews government’s $11 billion Melbourne Metro Tunnel.

Last February, Mr Frydenberg took the “extraordinary step” of placing an emergency heritage listing on the 19th century boulevard. He had until Tuesday to make that listing permanent.

The minister said doing so would not overrule the federal government’s decision in 2015 to give the project the green light without the need for environmental approval.

But he said it would prevent future development that would "interfere with the national significance" of the site.

“I looked at every particular angle as to how we could stop those trees being destroyed, but given the previous approval we were not able to prevent that from happening,” he said.

“But today's decision is a significant one in that for the first time these unique Melbourne places will be protected under federal law.”

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Called Melbourne’s Domain Parkland and Memorial Precinct, it covers 109 hectares south of the CBD between St Kilda Road and the Yarra River.

Along with the shrine and parkland it includes Government House and the Melbourne Observatory.

Mr Frydenberg said the removal of trees on St Kilda Road had "brought an urgency" to the listing – but that these places had been on the radar of the heritage council for some time.

The precinct is now the 114th place on the national heritage list.

Asked what sort of development the listing would prevent, the minister said future projects would have to be analysed on a case-by-case basis.

But he said it would have made the approval process which allowed the Melbourne Metro Rail Authority to chop down the trees – including elms dating back to the 1800s – “more difficult’ and the assessment process "more extensive".

“This absolutely adds an additional layer of oversight and protection at the federal level on the approval process for any actions that would interfere with the environmental, historic, cultural and Indigenous values of the site,” Mr Frydenberg said.

Parts of the precinct – including the shrine, observatory and Government House – are already listed on the Victorian Heritage Register.

But Australian Heritage Council member Dr Lyndon Ormond-Parker said the national listing would offer greater protection for the area in future.

He said a report on the site commissioned last February and publicly released on Sunday examined concerns about the impact of the Metro project on the precinct.

"It is very disappointing that some trees will be lost, but this national heritage listing gives permanent protection to the 109-hectare area," Dr Ormond-Parker said.

The Alyawarr man said it was "terrific" to see all of the memorial sites in the precinct recognised together.

He said it would be particularly important for the Aboriginal community given the inclusion of the King's Domain Resting Place – a commemorative burial place for the remains of 38 Victorian Aboriginal people who were repatriated from the Museum of Victoria in 1985.

Shrine of Remembrance chief executive officer Dean Lee said the organisation welcomed being included in the national heritage listing, five years after its submission to do so was turned down.

"We're delighted the site is being recognised for its memorial values for the past 84 years of honouring community service and sacrifice," he said.

"It's entirely fitting in the final year of the Anzac centenary for the value of this shrine to be recognised."

Mr Lee declined to comment on the metro rail project but said the authority had been "respectful of the shrine and its needs".

A nearby underground station to be built at the intersection of Albert Road and Domain Road, called Anzac Station, will feature a "floating" timber canopy that sits below the tram interchange.

The Melbourne Metro Rail Authority has promised to plant an extra two trees for every one removed, and suggests that they would be planted in improved soil conditions and with better irrigation.

Construction is slated to begin early this year and the authority estimates building the Anzac Station precinct will take about five years with surface disruption expected to be shorter than the overall construction time.

Last year's interim heritage listing drew an angry response from Victorian Public Transport Minister Jacinta Allan, who said the Turnbull government was "teaming up with the state Liberals to try to stop the Metro Tunnel".

But Mr Frydenberg called on the Andrews government to support the national heritage listing becoming permanent.

"It would be astonishing if they did not welcome the listing of these sites on the national heritage list, given their significance for all Victorians," the minister said.

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