The State Emergency Service received just under 1000 calls for assistance on Tuesday night, mostly related to trees crashing down onto homes and roads. 

Meanwhile, residents in low-lying areas of Myrtleford were told to leave their homes as the Ovens River swelled to six metres, threatening properties and caravan parks.

SES crews worked through the night, door-knocking homes.

Benalla-based SES management officer John Newlands said the Ovens peaked in Myrtleford about noon, and attention would now shift downstream.

"Our next focus will naturally be Whorouly, Markwood, [towns] down that way," he said.

"And then in Wangaratta tonight, we're understanding the peak could be from about 9pm onwards until daybreak."

Mr Newlands said isolated properties outside of the levy bank system in the Lower Ovens area would be prioritised.

In Myrtleford, one family was provided with emergency accommodation and 15 people took shelter with family and friends on Tuesday night.

Mr Newlands said one house was inundated while others had been cut off by rising waters.

Several roads across the north-east have been closed due to flooding, with police redirecting traffic.

Emergency services workers fear flood waters will continue to rise despite easing rain. More than 70 millimetres of rain has been recorded in the area since Tuesday morning. 

The SES is sending a special taskforce to Wangaratta on Wednesday to assist with local flooding problems.

An SES spokesman said an emergency relief centre has also been set up at Myrtleford's senior citizens' centre. 

"A number of caravan parks have been relocated," he said. 

"There's also a number of power outages up around that way as well."

More than 500 Myrtleford residents were without power on Wednesday morning. 

Residents in Charlton, in the state's north-west, as well as people living close to the Loddon River, near Bendigo, are also on alert. 

SES spokesman Stefan Delatovic urged motorists to avoid flood waters. 

"This weekend we saw a few more people driving through floodwater, so we just want to reiterate that it's really dangerous and a bad decision to make," he said. 

While there is lingering rain forecast for Melbourne on Wednesday, Thursday is expected to be mostly sunny with a top of 25 degrees.

- with Chloe Booker