Almost 2,000 people in central and western Victoria have been evacuated from their homes, as flooding hits large parts of the state for the third time in five months.

The entire town of Carisbrook in Central Victoria has been evacuated and locals say the whole town has been inundated.

The State Emergency Service (SES) says homes have also been flooded in Creswick, Clunes, Skipton, Charlton and Beaufort.

About 70 people fled their homes in Beaufort in the state's west this morning when the town's reservoir broke its banks.

Emergency alerts have been issued in Halls Gap, Great Western and Glenorchy.

Major flood warnings are in place for the Loddon, Wimmera, Avoca and Campaspe Rivers.

SES spokesman Trevor White says flooding in some parts of the state will be worse than the floods that hit in September.

"At this stage our advice from the bureau is that along the Loddon and Wimmera Rivers, it's likely that the impacts may be greater than they were in September," he said.

"We anticipate similar outcomes [to September] along the Avoca River."

The SES is warning communities downstream on the Loddon, Wimmera and Avoca Rivers will face the biggest threat in the coming days.

Mr White says downstream towns need to be vigilant.

"Although the weather system is moving to the east of Victoria, we need to remember that there will be downstream impacts on a number of these systems," he said.

"We'll be working with the hydrologist over the next few days to make sure we can provide timely information to communities to assist them in their preparation."

The SES has responded to more than 3,000 calls for help across the state since Tuesday.

Anxious wait

Evacuation centres have been set up in towns throughout central and western Victoria.

About 800 people who fled Carisbrook - the town's entire population - are sheltering in two relief centres in Maryborough.

Central Goldfields Shire chief executive Mark Johnston says locals do not know how badly their houses have been damaged.

"Some of the buildings won't have had inundation yet, but our sense is that many more will be inundated than won't,"

"We expect that to be in the hundreds."

In Charlton, about 15 elderly residents at an aged care unit have been evacuated.

In Skipton, the flooded Emu Creek has inundated homes and businesses.

Mayor Matt Makin says the flood levels seem to be higher than in September.

"Overnight the water has exceeded that sandbagging so there has been some flooding and inundation of a number of residences and shops in the town of Skipton," he said.

"We're still trying to quantify that, but it does seem to be worse than what happened in September last year."

Roads closed

More than 100 roads across Victoria are closed because of flooding.

A road bridge on the Wimmera River at Crowlands, east of Ararat, has collapsed.

Crowlands resident Steve Jardine says people were standing on the bridge and jumped off just in time.

"I was talking to some of the locals there, they were saying that they were standing on the bridge, or at the edge of the bridge and they could hear it creaking," he said.

"It just gave way."

The Midland Highway is closed at Creswick, the Western Highway is closed between Ballarat and Horsham and the Glenelg Highway is closed at Emu Creek Bridge at Skipton.

Dozens of local roads are closed in the Pyrenees, Hepburn, Corangamite and Central Goldfields Shires, and in the city of Ballarat.

The Great Ocean Road remains closed between Skenes Creek and Lorne.

Record rainfall

Kyneton and Maryborough in central Victoria have recorded their highest ever summer rainfall in the past 24 hours.

Claire Yeo from the Weather Bureau says up to 150 millimetres of rain fell in some parts of Victoria in the last 24 hours.

"A lot of locations in the west have actually exceeded their whole summer average in just five days," she said.