The worst of the latest Victorian storms has passed, the Bureau of Meteorology has said, with a storm that moved through Melbourne on Thursday bringing heavy rain to the state’s north overnight.

Shepparton received 44 millimetres of rain in two days and 42 millimetres fell in Kyabram, much of which fell in heavy downpours on Thursday evening.

There was also heavy rain west of Melbourne.

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However BoM senior forecaster Richard Carlyon said the worst of the conditions had moved through.

“It looks as though the humidity is starting to move out of the state it’s been pushed away by cooler westerly winds,” he said.

“We should see more settled conditions coming up for the weekend.”

The State Emergency Service (SES) did not see any significant damage from the torrential rain and hail which hit the city, causing flash flooding.

The weather bureau issued a short-lived tornado warning for the city on Thursday, after a funnel cloud was spotted near Tullamarine.

The SES’s Tim Wiebusch said they had hundreds of calls for help from people suffering from flash flooding.

“We haven’t had any significant damage reported as a result of the thunderstorms,” he said.

“It’s mainly to do with leaking roofs a few trees down and flash flooding.”

The worst affected areas were the bayside, CBD and north-west of the city.