Emergency warnings remain in place for multiple areas, including Shepparton, Murchison, Echuca, Kialla, Mooroopna, Orrvale, Charlton Barnadown and Elmore.
Early on Monday in Echuca, residents and holiday-makers were being told to immediately leave amid concerns people could become stranded by floodwaters.
Emergency Management Commissioner Andrew Crisp said communities such as Echuca along the Murray River could be under flood threat for four to six weeks, with workers and volunteers preparing for a long campaign.
Federal Emergency Management Minister Murray Watt said modelling indicated more than 9000 homes were inundated in Victoria's north and about 34,000 homes across the state could be inundated or isolated.
"It's quite likely we'll see a flood peak happen and waters recede, followed by another peak as different river systems come together," he told ABC TV on Monday.
Prime Minister Anthony Albanese, travelling to flood-hit western NSW on Monday, warned bumper wheat, fruit and vegetable crops in Victoria's food basin have been affected and it would inevitably lead to rising prices.
"The impact will feed into higher prices, most unfortunately at a time when inflation has already been rising," he told ABC Radio Melbourne.
The Goulburn River at Shepparton has risen overnight to 12.05 metres, with major flooding expected on Monday morning at 12.1m.
That is higher than the 1974 flood level of 12.09m, the Bureau of Meteorology says.
Images show buildings in the middle of town surrounded by a vast inland sea of brown muddy water and residents using sandbags to protect properties.
Mr Crisp said 56 requests for rescues were made overnight in Mooroopna and Shepparton.
Hundreds of homes in the area have been flooded along with another 800 to 900 homes in Rochester, where a 71-year-old man was found dead in the backyard of his home on Saturday.
Floodwaters have receded in Maribyrnong, where police confirmed an unoccupied house was looted on Monday morning.
It is believed a man wearing high-vis and a face covering entered the flood-hit home and stole items, before fleeing in a car with another two men waiting inside.
Melbourne Water has been directed to carry out a review of Flemington Racecourse's levee wall to determine whether it contributed to the flooding of properties in Maribyrnong and Kensington.
The Loddon River at Kerang is expected to peak on Tuesday and into Wednesday, with levels similar to the record-breaking January 2011 floods.
A warning has also been issued for the Wimmera River, with Horsham residents warned major flooding is possible on Monday and into Tuesday.
The Campaspe River at Barnadown, Rochester Town and Echuca peaked on Monday morning with major flooding occurring - higher than in 2011.
The Victorian State Emergency Service has received more than 4750 calls for help, including more than 500 flood rescue requests, since Wednesday when heavy rainfall lashed the state.
Disaster recovery payments have been made available to residents in 23 local government areas and a 250-bed camp will open at the former Mickleham COVID-19 quarantine facility.
About 100 ADF personnel have been deployed to help with evacuations and sandbagging.
Dozens of schools were closed across the state on Monday, including almost 50 in the northeast, almost 30 in the northwest and seven in the southwest. Early childhood services were also closed.
The Victorian health department has warned of the increased risk of bacterial outbreaks such as leptospirosis, which is caused when people come into contact with the urine of infected animals and can occur after flooding events.
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