Manuherikia River water user and high country farmer Andrew Paterson said these periods were "not bankable".
He wanted to upgrade his flood irrigation to a cleaner and more efficient spray system, but could not because the "banks won't lend".
Within the last 18 months the council and water users were working together and were on track to meet deadlines, he said.
"I think the [ministry] report came with an agenda. It had already pre-decided what they were going to do."
Otago Federated Farmers president Simon Davies said the recommendations put farmers in a "holding pattern" for an additional five years.
Many farmers needed to upgrade from flood to pivot irrigation, which was "better for everyone", but it would be difficult to prove loans could be paid off in five years.
"These farmers don't have an extra million dollars lying around."
Parker said he did not think the short-term consents should "cause much angst".
"They get their issue dealt with in the interim pending a longer term fix. That's all people can expect to achieve here."
Council policy committee iwi representative Edward Ellison said the overhaul suggested by the report was "long overdue".
"In my time there it was pretty evident that the planning framework was not fit for purpose."
Otago Fish & Game Council chief executive Ian Hadland said it supported the report's findings and recommendations.
"The current framework is the one which has seen Otago's rivers depleted on a scale
rarely seen elsewhere in New Zealand and this cannot continue.
"In the immediate, the ORC must ensure that decisions made under this framework will not be locked in for the long term. We owe that to future generations."