VICTORIANS have been warned the worst of the mega storm sweeping the state is yet to come, with at least 40mm of rain expected to fall across Melbourne overnight.

Emergency Services Commissioner Craig Lapsley warned Victorians to brace for a torrid Saturday.

"The forecasted rain for Saturday is in the hundreds of millimetres. It could go as far as 250mm in the northeast," he said.

Flash flood warnings have been issued for at least a dozen Melbourne suburbs.