Shepparton Incident Control Centre incident controller Ray Jasper said seven businesses had floodwater through them in Seymour on Monday.
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He also said authorities thought eight to 10 houses that had been flooded in the October 2022 flood and had not been fixed up and were not being lived in, also flooded in Seymour.
“It’s still sad for these houses to be flooded again,” he said.
Some streets in the town remained flooded on Tuesday morning.
The Goulburn River peaked on Monday afternoon at 6.8m — about 20cm below what had been predicted.
Forty-three people spent the night in the Seymour Relief Centre, with 12 caravans also parked up with occupants in them at the centre.
Three caravan parks and four motels in Seymour were cleared on Monday because they were in the flooded area.
Mr Jasper said the evacuation order would be lifted in the town when the river dropped to 5m, and at that time, the relief centre would also close.
Yea endured what was described as a one-in-100-year flood.
Six homes in the town were flooded.
The town was cut off on Monday by floodwater, but roads reopened on Tuesday morning.
In Avenel, Hughes Creek came up quickly on Monday, but Mr Jasper said no houses were flooded.