A day after plans to scuttle Melbourne's proposed Apple flagship store failed, the government says it is pushing on with the controversial development.

Planning Minister Richard Wynne has thrust his support behind the tech store at Federation Square after a Greens upper-house motion to block it was struck down 34-4.

Despite an online petition to abandon the plan attracting more than 53,000 signatures, Mr Wynne reaffirmed the Andrews government’s commitment to the project.

“The Apple store is going ahead,” he told ABC radio on Thursday.

“We are continuing to have very productive conversations with the City of Melbourne around some design modifications.”

The proposal would see the city’s central riverside precinct become home to the southern hemisphere’s only flagship Apple store but would require partial demolition of Federation Square.

“This will open up the square,” Mr Wynne said.

“I’ve looked very carefully at the Apple development. It is a good development for the city and indeed the original architect for Federation Square not only endorsed the plan … (so) did the state architect.”

But the Greens are not backing down.

“This fight isn’t over. We’ll continue building public support to show the Andrews government exactly how unpopular this decision is,” Member for Melbourne Ellen Sandell said.

Coalition members in the upper house did not vote in favour of the Greens’ motion despite Opposition Leader Matthew Guy previously calling the plan “an abomination”.