The council voted six to five in favour of Cr Michael Laws' motion in which minimum flows and NPSFM work would need to be done concurrently for these three catchments.
Council chairman Stephen Woodhead said the council would now need to assess the implications of the motion.
It seemed it would be "impossible" to complete the work in time and would put huge strain on council resources, he said.
"There are some implications that the community and councillors don't understand at this point."
Staff said minimum flows and NPSFM work should be done separately as the latter was a large body of work.
This would have meant irrigators in some catchments would need two different consents over two plan changes.
Mr Woodhead said even with the new motion irrigators would still likely need another consent the during the NPSFM work.
Otago Water Resource Users Group Manuherikia subcommittee chairman Gary Kelliher said it was "relieved" at the outcome as "a sensible position has been found".
Concerns raised by councillors against Cr Laws' motion could "easily be worked through" by the group, he said.
More than 50 members of the public watched the debate at the ORC chambers yesterday.
Otago Fish and Game spokesman Niall Watson said it was critical the minimum flow plan framework was developed soon and included the community beyond just irrigators.
Cr Bryan Scott said in his view the setting of a minimum flow and allocation limits were separate processes.
Cr Graeme Bell said the staff who wrote the report did not understand water allocation or how to manage it.
Cr Michael Laws said the council was setting limits based on an unproven assumption there was a threat to the Manuherikia River's health.
Cr Gretchen Robertson said setting minimum flows was needed "as soon as possible".
