Crown Resorts saved itself millions of dollars under a special deal granted to it by Planning Minister Richard Wynne to build Melbourne's biggest skyscraper.

The gambling giant will pay $72 million in fees and taxes for its One Queensbridge Tower on the banks of the Yarra River.

An artist's impression of Crown's approved 90-storey hotel and apartment tower in Southbank. Credit:Melbourne City Council

But a Melbourne City Council report released on Thursday shows Crown would have had to pay $133 million if the project had been assessed under new rules brought in by Mr Wynne last year.

Mr Wynne put in new laws in November requiring companies that want approval for large towers to pay compensation, in the form of improved public space, affordable housing or other offsets.