Controversial plans to build a flagship Apple store at Melbourne's Federation Square have been redesigned following criticism that the original draft was ugly and created without public consultation.

In December the Victorian Government revealed the three-story Yarra Building at Federation Square would be demolished to make way for the tech giant's two-storey concept store.

There was a strong public backlash to the original plans, which featured a copper-coloured pagoda-style facade that some dubbed a 'Pizza Hut pagoda'.

The original pagoda design was roundly criticised when it was announced. ( Supplied: Victorian Government )

A new design has now been unveiled, transforming the building into a rectangle with a glass facade on the ground floor and a coloured mesh facade on the second floor.

It would include a publicly accessible balcony that overlooks the Yarra River, and an amphitheatre for public performances.

The chief executive of Federation Square, Jonathan Tribe, said the new design was "more sympathetic" to the style of the existing space.

An artist's impression of the view from the balcony over the Yarra River. ( Supplied: Apple )

"The original design was very much a concept plan and was always subject to refinement," Mr Tribe said.

But the new design is already copping criticism.

The National Trust said while it was encouraging that Apple was open to redesigning the building "it did not respond to the fundamental concerns that were proposed about the demolition of a significant building".

"The updated design has also been prepared without community consultation with its most important stakeholders — the people of Victoria," chief executive of the National Trust Simon Ambrose said.

Community groups echoed that sentiment.

"We think Apple doesn't fit in Federation Square," Tania Davidge from Citizens for Melbourne said.

"Federation Square should be primarily based around people, not Apple products."

The new building will replace the current Yarra Building. ( Supplied: Apple )

But Mr Tribe said including the store at Federation Square would help bring "innovation and creativity" to the public space.

"[Apple] will run over 73 sessions a week around music, photography and art," Mr Forbes said.

The latest plans will be submitted to the City of Melbourne for public consultation.

"I still think there is some tweaking to be done," Mr Tribe said.

When the Government spruiked in the original plans, it said the development would attract an extra two million visitors a year to the area.

Work was to begin on the concept store next year and finish in 2020.