Victoria's mild start to winter has come to an abrupt halt as a "winter weather bomb" caused destructive winds, rain, hail and blizzard conditions in the alpine areas, the Bureau of Meteorology has said.

Forecaster Kevin Parkyn said the intensity of the weather system caused the pressure to drop, bringing winds of up to 130 kilometres per hour and a storm surge along the coast.

While the destructive winds did not last long, the damage across the state was significant.

"In that time it saw many centres across the state register wind gusts of between 100 and 110kph," Mr Parkyn said.

"The highest or peak wind gust was recorded at Cape Otway, where 128kph gusts were recorded earlier this morning."

Melbourne's bayside suburbs were not spared, experiencing peak wind gusts of 110kph on land and 120kph over the water.

Sorry, this video has expired Yarra River overflows along Melbourne's Southbank

The State Emergency Service responded to more than 2,500 calls across the state and 1,600 in Melbourne alone.

There were about 700 calls related to building damage.

Spokesman Trevor White said he expected the calls for help to continue as people returned home from work to find more damage.

"We expect our [SES] crews, with CFA (Country Fire Authority), DEPI (Department of Environment) and MFB (Metropolitan Fire Brigade) will be working hard through the night and also into tomorrow to clear the damage," he said.

Emergency crews had a number of reports of injuries during the wild conditions, with a number of people being hit by flying debris.

One person was injured when a wall collapsed at Yarraville and there were reports of minor injuries from people being hit by flying trampolines and garden furniture.

Another person was struck by roof sheeting in the CBD and there were several cases of trees coming down on cars.

Mr Parkyn said the worst of the weather was over but there were more high winds forecast for the rest of the week.

"The Bureau of Meteorology is likely to issue severe weather warnings for the rest of the week as the state continues to be buffeted by winter weather systems," Mr Parkyn said.

There were whiteout conditions in the Alpine areas and up to a metre of snow is forecast by the end of the week.

Flooding at Melbourne's Southbank precinct

Ponyfish Island, a bar which normally floats on the Yarra River under the pedestrian bridge in the CBD, was swamped with knee-high water as the river swelled due to unexpectedly high tides combined with the bad weather.

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Spokesman Josh Marsh said they would have to wait until the water receded before they could assess the damage.

"We could see the water rising but we've had a few minor floods before which weren't an issue but this one kind of caught us by surprise," he said.

"It happened very quickly.

"Luckily we had a flood management plan which we put in place and we just had to get off the island as quick as possible."

The wharf on the Yarra River, where cruise boats pick up tourists outside Southgate, was also flooded.

At least four ticket booths were swamped and water was lapping at the bottoms of benches along the wharf.

Steven Michalas, of Melbourne River Cruises, said it was the worst flooding he had seen in his 13 years working with the company.

He said they had been expecting a high tide but this one reached 1.75 metres.

"It was expected to be a 0.88 [metre] tide which isn't too bad, but the tide came up very early," he said.

The wharfs on both sides of the Yarra were flooded but it was nowhere near high enough to flood the promenade outside Southgate or the shops inside.

Power gradually being restored

At the peak of the storm, up to 80,000 people were without power.

Damien Batey of United Energy said the worst hit areas were Frankston, the Mornington Peninsula, Sorrento, Mulgrave and Ringwood.

"We've also had quite severe wind gusts of in excess of 100kph," he said.

"That's caused a combination of wires clashing and also situations where power lines have [fallen to the] ground."

Power has been restored to most homes except for some customers in Sorrento, Beaumaris and Bittern.

Lyall Johnson, from Powercor and CitiPower, said up to 35,000 of their customers lost power.

He said if people returned home from work and did not have power they should not panic but it may take a bit longer to get about 238 customers near Bendigo back up and running.

"There is an area near Bendigo where we're really not sure we're going to get people back on much before [this evening]," he said.

On public transport, most lines were expected to be cleared for the afternoon peak after disruptions on tram and train lines caused by fallen trees.

The worst damage was on the Belgrave line near Upper Ferntree Gully.

Trains will only run to Bayswater station until the clean-up is completed.