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In a report to council this week Mr Woodhead said it needed to speak to landowners about protocol after bales floated away in the Taieri last month.
They could have landed in waterways, become caught by infrastructure such as bridges, or been left sitting in drains.
He said yesterday ''hundreds'' of bales were washed away last month.
''These bales can and have caused problems for infrastructure such as bridges, culverts, flood gates, pump stations and ditches where they end being trapped.
If they became stuck in culverts it could have a ''significant'' impact on flooding.
''Occasionally they end up in the actual river and there is often plastic wrapping left lying around when they get damaged as they float into fences and trees.''
Bales needed to be moved to higher ground and out of the flood path where possible, he said.
''Often the baleage is not usable after being caught in floodwater and so is a significant waste of feed, nutrients and money for the farmers.''
The council discussed the issue several years ago with landowners, but they needed an update, he said.
Otago Federated Farmers president Simon Davies said
the problem last month was the flood hit at an ''unexpected time''.
Most farmers had made the baleage just days before and so hadn't moved or stacked it.
''I heard of one farmer who was away and several neighbours in his absence were trying to pick up as much as possible. It's an absolute hazard, no doubt about it.''