Residents of 101 suburbs including those supplied by Yarra Valley Water and South East Water were on Saturday told to boil water because it may not be safe to drink, and posed a risk of gastro.

The warning applies to about 200,000 households.

"Water agencies are working around the clock to check water quality and that boiled water notice will come off as soon as it is safe to do so," Premier Daniel Andrews said.

The instruction applies for all water used for consumption, washing, baby formula, food preparation and making ice.

"It's very important people have that extra precaution ... so that people aren't getting sick because of the unavoidable issues with power at one particular water treatment plant."

Parts of Victoria were hit by wild storms on Thursday night, costing three lives including four-year-old boy Ayan Kapoor, who was struck by a tree in suburban Melbourne.

A 36-year-old woman in Fernshaw in regional Victoria was killed after a tree hit the ute she was in and a 59-year-old man died when a tree fell on his car as he was leaving a shopping centre in Belgrave.

As the cleanup continues on Saturday the weather bureau has warned of another rough front due on Sunday.

Mr Andrews said emergency crews received about 3000 calls for assistance after the recent storms and all but about 100 had been finalised.

On Saturday morning some 13,000 homes and businesses remained without power, down from 180,000 at the peak of outages.

Australian Associated Press