Melbourne emergency services said they received more than 1,000 calls for help and rescue workers had to use boats to save about a dozen people stranded on car roofs when flashfloods inundated a major city freeway.

Weather Bureau duty forecaster Dean Stewart said the storms which moved onto Melbourne's northern and eastern suburbs around midnight were the city's worst in a century.

"Parts of the north and eastern suburbs of Melbourne had more than 100 millimetres of rain over two hours," he said. "This is a once in 100 year event."

The bureau's senior forecaster, Ken Dickenson, described the storm as "freakish".

Callers to local radio stations reported hail the size of golf balls pummelled the eastern suburb of Lilydale while the Victoria State Emergency Service said hundreds of homes and businesses had been hit by flooding or damage from collapsed roofs or falling trees.

Ambulance services reported no injuries.

The weather bureau said more storms were expected to hit parts of Melbourne later Wednesday.

TERRA.WIRE