Victoria State Emergency Service chief operations officer Tim Wiebusch said Rochester was emerging slowly from its worst flooding on record, well above the 2011 peak.
Speaking on Monday morning, Mr Wiebusch said the Campaspe River had receded to moderate levels in Rochester.
He said it was too early for impact assessment teams to start work, but early indications suggested 85 per cent of the town was inundated.
On the Goulburn, the water level in Shepparton and Mooroopna peaked at 12.06m on Monday morning despite the city bracing for an expected peak of 12.2m.
Mr Wiebusch said that extra 14cm made a “significant difference” to the number of homes and businesses that would be affected by floodwaters.
Mr Wiebusch said there were about 4000 properties isolated or inundated in Shepparton and Mooroopna, but said people should expect the water to stay high for four or five days.
“It will be Thursday into Friday before the water can recede, and in regards to the causeway ... it will need to be assessed before it can be opened,” he said.
“It will be some time before the Goulburn goes below the major level of 11m.”
Mr Wiebusch said the Broken River at Orrvale had peaked at 8.35m and would remain at major flood level for a few days.
In Seymour, the Goulburn River has receded despite water coming out of Lake Eildon.
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