The Murray River surpassed the 1993 flood level of 94.77 metres above sea level at Echuca on Saturday night and is expected to peak around 95m on Sunday evening into Monday.
SES Victoria's Tim Wiebusch said 20 homes in and around Echuca Village were door-knocked on Saturday night after water seeped through a levee.
"Those levees, whilst they're holding at this point in time, do continue to be a vulnerability for that particular community," he told reporters on Sunday.
"Our advice is to evacuate, rather than becoming isolated or impacted in that area."
The evacuation alert covers between 500 to 700 people living across 250 properties in the area.
Further northwest, the London River at Kerang has peaked below the 78m forecast at 77.94m, but the threat has not passed.
Water levels have only slightly receded and aren't expected to subside for five to seven days, keeping the community isolated.
A levee on the southwest corner of the town has been breached, sending water into an industrial area, caravan parks and about 20 homes.
"The broader part of Kerang, at this stage, is high and dry," Mr Wiebusch said.
About 50 to 60 per cent of the 3000-strong local community have remained behind to protect their properties.
Premier Daniel Andrews has pleaded with residents to heed the evacuation advice.
"People give that very careful thought. We don't issue those warnings lightly," he said.
About 50 people from flood-hit communities across the state have taken refuge at the Mickleham quarantine centre, Mr Andrews said.
More than 65 flood warnings remain active in Victoria.
More rain is forecast for the flood-hit state as a low pressure system moves over northern Victoria on Sunday.
The state's northeast and far northwest are tipped to cop the brunt of the falls and the Bureau of Meteorology predicts the system will bring wet weather to southern Victoria early in the week.
The SES has received more than 8700 calls for help since the weather emergency began and more than 750 flood-related rescue requests.
Flood warnings remain for towns along the Loddon, Goulburn, Campaspe, Avoca, Barwon, Kiewa, and Ovens and King rivers.
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