Water could rise to match 1993 flood levels in the next 48 hours to Sunday and even higher by Tuesday.
SES chief operations officer Tim Wiebusch said towns along the river had another chance to evacuate before that happened.
However it is too late to leave the smaller towns of Barmah and Lower Moira, he told ABC TV on Friday.
On Friday major flood warnings were issued for the Avoca River downstream of Charlton and the Murray River downstream of Tocumwal.
Isolated thunderstorms could deliver up to 30 millimetres of rain for already drenched parts of northern Victoria on Friday.
Flooded towns downstream of Lake Eppalock, like Rochester, could face a new threat if forecast thunderstorms set in over the weekend.
Residents in Echuca who have not already evacuated have been told to limit water usage, including showers and washing machines, to reduce the amount of water sent to sewers while flood levels are high.
Authorities there have spent days building a makeshift flood levee more than two kilometres long through the town.
Up to 50 properties in Kerang in the state's north could be inundated when the floods peak on Friday.
Residents there are unable to leave after a bridge connecting the town to a major highway was closed on Wednesday night, but authorities believe a flood levee will protect the town centre.
Rochester and Murchison residents have been told it is not safe to return.
Eighteen volunteers from the Queensland SES have been deployed across Victoria, while up to 400 ADF personnel are also helping with sandbag distribution and doorknocking.
The Victorian government on Thursday announced $6.5 million for health protection measures in flooded communities, including free Japanese encephalitis vaccines.
Two hundred hospital staff and 20 pharmacists will be sent to Victoria's flood-ravaged regions for the next three months to help the worst-affected public health units.
On Thursday two men were arrested over a robbery at a flood damaged home in the inner Melbourne suburb of Maribyrnong, which was inundated last week.
A 26-year-old Sunshine West man was charged with 12 offences and a 33-year-old was expected to be charged on summons.
Police are seeking a third man who may be able to help them with the investigation.
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