The Bureau of Meteorology has issued a severe thunderstorm warning for parts of the state's northern country and north east, with flash flood warnings in place for Euroa and Wangaratta.

Senior forecaster Richard Carlyon said heavy rainfall hit Wangaratta Airport, about eight kilometres outside the city centre, from about 8pm.

"Wangaratta's copped the most rain," he said.

"They've had 69mm.

"Another place towards Euroa, Greta West - they've had 60mm.

"Most of the storms in the state weakened out but two clumps of cells up in the north east of the state have been slow moving and produced this heavy rain."

Earlier, heavy rainfall hit much of the state's east, from Yarra Glen, 45 kilometres east of Melbourne across to the NSW border.

Around 33mm of rain has fallen at Mt Elizabeth and 22mm at Snowy Range in the Eastern Ranges.

Mr Carlyon said the rainfall at Wangaratta had been very localised.

"The storms were just sitting over the airport, where that 69mm was measured," he said.

"It's well over monthly average rainfall. This time of year the average is around 40mm.

"At Wangaratta, 61 of that 69mm was in an hour. They've had more than a month's rain in just an hour tonight."

The State Emergency Service advised people in affected areas to keep clear of creeks and storm drains and avoid any attempts to cross through flood water.

Both the Bureau of Meteorology and the SES urged local residents to stay informed of updates on the BOM or EmergencyVic websites or ABC local radio.