A three kilometre long dirt barrier was constructed to protect the centre of town from the worst of the disaster and people living on the so-called 'wrong side' were told their houses were likely to be inundated.
Emergency Management Commissioner Andrew Crisp said a couple of hundred homes had been impacted by flooding in Echuca so far.
Residents were left "gobsmacked" by the decision to pump floodwater away from the 'right side' towards houses on the 'wrong side' on Tuesday morning.
Resident Jemima Lewis told ABC Radio it was "just unfathomable" those houses would experience further flooding.
"It's just disgraceful to see that in this community and in this area after everything we've been going through," Ms Lewis said.
"To see my neighbours having the pumps turned into their backyards instead of sensibly down towards the current where the water can keep moving."
Mr Crisp said he asked whether the excess water could instead be directed somewhere else but added residents were warned their houses would be impacted.
"We need to get to a point (where) we need to assess what has actually occurred if this levee holds and then at a point in time there will be further discussions with the community," he told reporters.
Some affected residents are reportedly considering legal action.
On Tuesday the Campaspe Shire Council released a statement saying Emergency Management Victoria was responsible for the wall and it was not consulted on its location or design.
Mr Crisp said he understood local government had been engaged in discussions about the levee.
There have been 950,000 sandbags distributed across Victoria in the past seven days, including 195,000 at Echuca.
Fifty-one flood evacuees have been housed at the Mickleham quarantine facility as of Tuesday morning.
There were 70 warnings issued across the state including evacuation orders for Echuca, Echuca Village, Kerang, Barmah, Lower Moira and Bunbartha.
Bureau of Meteorology Senior Meteorologist Kevin Parkyn said up to 50 millimetres of rain could fall over several days in north eastern parts of the state when wild weather returns from Sunday.
"There's no doubt that October will smash the rainfall record across the northern plains," Mr Parkyn told reporters.
"There will never have been a wetter October in our record books."
Recovery efforts across central Victoria are about to ramp up, particularly at Rochester and Mooroopna, which were badly damaged almost a fortnight ago.
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