The Bureau of Meteorology has issued a thunderstorm warning for the area, stating the "liklihood of damaging winds and heavy rainfall that may lead to flash flooding... locations which may be affected include Shepparton, Wodonga, Wangaratta, Traralgon, Moe and Bairnsdale."

Melbourne was lashed briefly by storms this morning, said the Bureau, with the city receiving 3 millimetres of rain.

"There wasn't much that moved through the city," said senior forecaster Richard Carlyon. "At about 9am there was a couple of heavy downpours.

"In the southern suburbs there was some falls of about 10 millimetres. The city and northern suburbs didn't receive much at all."

Mr Carlyon said that Mt Gregory in the Upper Yarra had received about 20 millimetres and Mt Hotham about 15 millimetres.

However, the storms caused little damage with the State Emergency Service reporting it had only received four calls for assistance.

Mr Carlyon said this afternoon's falls in the state's east would vary from region to region.

"We could have thunderstorms and falls of 20 to 30 millimetres possible but generally falls throughout the region will be 5 to 15 millimetres."