Heritage Victoria executive director Steven Avery has recommended the public space be protected for its "historical, architectural, aesthetic, cultural and technical significance to the state".

Apple's plans for its flagship store - one of only five in the world - were approved by Premier Daniel Andrews last year, but public opposition has been vehement.

A final decision on its inclusion on the register will be made by the Heritage Council of Victoria, following a 60-day public consultation period.

Heritage Victoria says if it is included, "this would not prevent future use or development".

However, Apple would require a heritage permit, which may include conditions that could change its design.

Apple declined to comment.

The store was announced in December without public consultation and is expected to open in late 2020 with a 20-year lease.

Premier Daniel Andrews has previously said Melbourne should embrace the store or risk it being based in Sydney.

The National Trust of Australia backed Heritage Victoria's recommendation, saying it did not oppose development at the square, as long as it was appropriate.

"We are confident inclusion on the Victorian Heritage Register will not stand in the way of Federation Square's day-to-day operations," CEO Simon Ambrose said.

"We support appropriate permits and exemptions that will ensure it continues to thrive as a vibrant place of gathering and celebration."

Australian Associated Press