The Bureau of Meteorology is warning for damaging winds, heavy rainfall and flash flooding in some areas.

Duty meteorologist Stuart Coombs said short-lived storms were popping up throughout central Melbourne.

"This is a situation that changes every 30 minutes," he said. "They go on for their life-cycle and then break apart."

The storms were expected to ease on Sunday night before heading over the bay towards Frankston.

Outside Melbourne, Mr Coombs said a larger, more intense storm had hit parts of West Gippsland.