Evacuation alerts have been upgraded for Shepparton, Orrvale, Kialla West, and Mooroopna to reflect it is too late for residents to leave those areas.

The Midland Highway, also known as the Mooroopna Causeway, was slated to be closed on Sunday but authorities announced it would close between Mooroopna and Shepparton from 6.30pm on Saturday.

Properties in the region are expected to be impacted overnight Saturday.

The Goulburn River is expected to peak at 12 metres at Shepparton on Tuesday, making the flood the area's worst in decades.

An emergency evacuation directive has also been issued for Echuca and Echuca Village, with authorities wanting residents to get out by last light on Saturday.

Some residents in Echuca could be away from their homes for many days as a second peak is expected mid-to-late next week.

A 71-year-old man was found dead in floodwaters in the backyard of his High St home in Rochester in Victoria's north earlier on Saturday, but police were unable to reach the property as it was cut off by floodwater.

An evacuation order was also issued for Charlton Township at the foothills of the Great Dividing Range. It is also too late to leave the towns of Murchison and Murchison East.

Victoria Police Assistant Commissioner David Clayton said officers remain in evacuated areas to prevent looting.

"We anticipate that in coming days we're going to see some of the largest evacuations that we have ever seen," Mr Clayton told reporters.

Charlton resident and business owner Lindsay Patullo said water was already lapping at the door of his massage clinic on Saturday afternoon.

"It's still a very nervous wait as to what's going to happen," he told AAP.

The business was badly damaged in the 2011 floods and he was bracing for it to happen again.

"It would be the second time in eleven years if we go under but yeah, we'll see what happens, it's our livelihood" he said.

"It'd be heartbreaking to go through all that again."

By Saturday morning more than 460 homes were damaged by floodwater rising above floor level and around 500 properties remained isolated.

The SES has performed about 350 rescues over the flood emergency.

Of those rescues, 160 happened at properties in Rochester when residents who chose to remain in their homes had to be saved, while 150 involved people being rescued from stranded vehicles.

Fourteen relief centres and 55 sandbag collection sites have been established across the state.

The extent of the damage to hundreds of homes in inner Melbourne is just starting to become clear after the Maribyrnong River breached its banks on Friday.

Member for Maribyrnong Bill Shorten said many houses and a lot of community infrastructure had been damaged.

"I think that people here knew the theory of flood damage, but because it hasn't happened in a couple of generations of this significance I think it's a shock," Mr Shorten told ABC News.

Premier Daniel Andrews said defence personnel were assisting with the emergency across regional Victoria and up to 60 additional ADF experts will help with the clean-up in coming days.

Some contractors working on major infrastructure projects have paused construction to carry out repair work in flood-affected areas.

Mostly dry conditions were forecast until Tuesday across Victoria, however flooding is expected to return late in the week.

Australian Associated Press