Flash flooding and hailstones up to 4cm lashed the area during the violent storm, which hit about 4.30pm.

Bureau of Meteorology senior forecaster Scott Williams said parts of Shepparton resembled a war zone this morning, capping a wild weekend of weather across Victoria.

"Shepparton copped very, very severe winds. There's a possibility of even tornadoes in it because massive trees were uprooted. As someone said, it looks like a bit of a war zone," he said.

"It was a storm that wasn't much short of what what we had in Melbourne (on Saturday)."

However, the Bureau was unable to provide the top wind speed in the area as Shepparton's automatic weather station stopped working at 4.30pm, when it was possibly hit by lightning.

State Emergency Service (SES) spokeswoman Kate Millar said the organisation received 224 calls for assistance in Shepparton between 7pm and 8pm yesterday.

"A lot of the calls were for building damage and trees down, a ceiling collapse and buildings flooded," she said, adding that back-up SES crews from New South Wales and South Australia had been called to provide assistance in Victoria.

Power was cut to about 45,000 customers around Shepparton when the storm hit, Powercor corporate affairs manager Hugo Armstrong said.

About 1500 customers remained without electricity today, and power to some homes would not be restored until tomorrow.

‘‘Northern Victoria has really borne the brunt of this,’’ Mr Armstrong said.

‘‘We have got a lot of lines down, cross arms are broken, some poles need replacing.’’

He said about 50 customers in Melbourne remained without power after Saturday’s storm.

The SES had received 5800 calls for assistance across Victoria since Saturday afternoon, many of them in the Melbourne area.

Mr Williams said 24mm of rain had been dumped on Melbourne's CBD since 9am yesterday.

Wind gusts of up to 100km/h have been forecast for the alpine region today, and winds of up to 60km/h forecast for other parts of the state.