And farmers in the Riverside Rd area say they will seek answers from the Otago Regional Council about why it lowered a floodgate when it did.
They say the council did so before predetermined Taieri River flow trigger points were reached.
Farmers say properties are as a result wetter and likely to remain under water for longer, which will destroy winter feed crops and force them to find alternative grazing.
The gates were propped up before 5am on Wednesday.
ORC environmental engineering and natural hazards director Gavin Palmer said police investigations into who raised the gates were continuing.
Taieri farmer Colin Scurr said his property was extremely wet but starting to dry out as the river dropped.
"The fact extra water got through with the gates down is a concern."
He hoped the regional council would meet farmers to discuss the operation of the floodgates.
Otago Federated Farmers chairman Mike Lord urged people to cool off over the floodgate issue, and said tension would not help resolve the issue.
Extensive and prolonged flooding of the Owhiro Stream has compelled sharemilker Duncan Wells to send half his herd - 300 cows - to Hillend, in South Otago, for winter at a cost of about $60,000, which will be shared with the owner of Mr Wells' farm.
Those cows were to have stayed on the farm of his employer Alan Scurr, but Mr Wells was concerned the quality of flood-affected feed might not be adequately nutritious for pregnant cows through late winter.
The swollen Owhiro Stream also caused problems on Allan Kirkland's Riverside Rd farm, with an estimated 84ha of his farm land still remaining under water yesterday.
Mr Kirkland intends trying to winter all his cows on his farm as usual, but says he might have to reassess that plan at a later date.
Mr Kirkland said while his farm received extra protection from the Taieri River, the Owhiro Stream caused problems.
The stream's floodgate into the Taieri River appeared to have been closed earlier than it had been closed in the past, but there was more run-off from land developments in Mosgiel and off the hills.
Farmers have also lost baleage.
It usually sells for $60 to $65 a bale, but is now costing up to $100 a bale.