A fast-tracked heritage application for Federation Square could be a roadblock for the government’s Apple store and Metro Tunnel projects.

But Premier Daniel Andrews disputed heritage registration could derail construction on the Town Hall metro station at the square.

He also questioned the heritage value of the site, which opened in 2002, but said Heritage Victoria should be left to do its work.

The National Trust on Wednesday announced it had fast-tracked a heritage nomination for the square “as a place of historical, architectural, aesthetic and social significance to the state”.

Additionally, the lack of transparency has been concerning, with no attempt to consult Victorians – the very people who Federation Square was built for,” trust CEO Simon Ambrose said.

Mr Ambrose also urged Federation Square to come up with a masterplan, subject to public consultation, as a matter of urgency.

The Apple ‘concept store’ was announced in December without any public consultation.

Demolition or redevelopment could still go ahead even with heritage registration, but it would require a permit from Heritage Victoria.

The nomination imposes a 60-day interim protection on the site.

Tourism Minister John Eren said it would not stop the government delivering Metro Tunnel “and other vital projects that are good for Melbourne and good for jobs”.

“It would be unprecedented to heritage-list a site that is only 16 years old, and to do so could lead to significant implications for future projects.”

Mr Andrews shrugged off the state significance of the site.

“It’s not necessarily what I would call a heritage asset,” the Premier said on Wednesday.

The Heritage Act does not define how old a site needs to be.

Mr Andrews said the Metro Tunnel works were “proceeding at pace”.

“There’ll be no disruption because we get things done. It’s as simple as that.

“I just don’t see this as an issue and the advice I have from those who are doing that work is there is no impact on Metro Tunnel.”

Heritage Victoria will provide a recommendation – after assessment and public submissions – for Heritage Council of Victoria to make the final decision.

Tania Davidge, from advocacy group Our City, Our Square, said it was “a really interesting turn of events”.

“I think the nomination for the heritage register allows us to take stock and to really think hard about what Federation Square means to all of us,” Ms Davidge told The New Daily.

“If the government won’t recognise Fed Square’s importance, I hope Heritage Victoria does.”

She said the Town Hall metro station design could be integrated better with the site.

The station designs were released in May.

Federation Square is on the trust’s Register of Significant Places, as the state’s premier civic and cultural space.

“Federation Square is one of our finest examples of 21st century architecture, and it has become a place where the people of Victoria and visitors can celebrate our history, diversity, identity and culture,” Mr Ambrose said.

“We think that it has architectural, aesthetic and social significance to the state of Victoria, and it’s a very, very important place for all Victorians.”

The trust made the heritage nomination after 12 months of consultation.

A redesign for the Apple store was released last month.