Melbourne's Federation Square is not a "heritage asset", according to Victorian Premier Daniel Andrews, but the site will still be considered for a protection listing.

The National Trust’s Victorian division has nominated the CBD landmark for inclusion on the state’s Heritage Register. It’s a move prompted by major developments at the site including a controversial Apple flagship store and the entrance for a new train station.

The trust said the nomination was made because of “a lack of transparency” and “no attempt to consult Victorians” about proposed changes.

“This is an important place for all Victorians and we want to make sure that it’s protected into the future,” National Trust Victoria chief Simon Ambrose told reporters on Wednesday.

“The National Trust is not about anti-development, we’re about making sure that places are preserved and looked after and appropriate development takes place.

“I’m not an architect, so I don’t deign to say what is an appropriate design at all, what I’m saying is there should be a master plan for Federation Square, there should be appropriate consultation.”

Mr Ambrose insisted the process of nomination started more than two years ago and pre-dated Apple’s December announcement, while the Metro Tunnel is already underway.

A heritage-listing also means any future development at the Federation Square site would need approval from Heritage Victoria.

The square is only 16 years old.

“It’s not what I would necessarily call a heritage asset … (but) … let’s let Heritage Victoria do their work,” Mr Andrews said, adding that the nomination would not affect Metro Tunnel works.

“As for the Apple store, that’s a matter for Heritage Victoria.”

Tourism Minister John Eren on Wednesday said it would be “unprecedented” to list a site that is only 16 years old.

Mr Andrews has previously said Melbourne should embrace the Apple store or risk the global firm instead choosing Sydney.

Attempts by the Victorian Greens in parliament to revoke planning permission for the store failed, but tens of thousands of people had signed an online petition against the change.

Consideration for heritage listing will take about 60 days, Mr Ambrose said.

By Kaitlyn Offer and Andi Yu