The Greens' chances of capturing inner Melbourne seats at the state election have taken a tumble after Premier Denis Napthine all but confirmed the Liberals would direct preferences to Labor.

Dr Napthine told 3AW this morning that the final decision on preferences would be made by the party's administrative wing but said he would have input on where to put the Greens.

"Let me say that the Greens aren't my favourite party, I don't think they act in the best interests of Victoria as a whole," he said.

The Premier also poured cold water on a potential preference deal with Geoff Shaw in Frankston, as the Coalition hopes to win the seat over Labor.

"We certainly wouldn't be putting Geoff Shaw high on our preference list but then again we wouldn't be putting the Greens high on our preferences either," he said.