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However, the minister has rejected the recommendation to extend the council's timeframe for major water work, saying it is not Parliament's responsibility to fix its ''non-compliance with the law''.
The ministry today released the findings of an investigation, which was launched in July, into whether the council was adequately executing its role in freshwater management and allocation.
It partly relates to the council's ability to transfer hundreds of century-old water rights into resource consents by 2021.
Prof Peter Skelton's report recommends the deadline be extended, through changes to the Resource Management Act, so the new consents were not granted within the council's current ''inadequate'' water plan.
Mr Parker rejected this idea. He was frustrated at the council's ''very slow'' work, he said.
''Given it's the failure of the regional council to meet a 30-year transition period it ought to not be Parliament's responsibility to change the law to meet the needs caused by their non-compliance with the law.''
The report says the council suffered from an underinvestment in science, planning and hydrological modelling.
''There is a lack of clear and robust minimum flows and a failure to address over-allocation.''
It was therefore not in a position to meet its deadline, the report said.
In a letter to the council, Mr Parker said the investigation identified the need to ''overhaul the entire planning framework'' of Otago.
Mr Parker told the Otago Daily Times he was careful to acknowledge the problems were a ''long time in the making''.
''The current council is co-operating with Prof Skelton.''
The council must publicly notify a review of its Regional Policy Statement by November 2020, and confirm a new land and water regional plan for Otago by December 31, 2023, he said.
The council had already started both of these reviews.
However, Mr Parker also recommends it create another plan change by March next year through which permits can be turned into consents in the interim.
These would be for a maximum term of five years, or until the council has completed its wider water plan, through which the new consents could then be processed through.
Council chairwoman Marian Hobbs said she acknowledged inadequate work in this area in the past.
The council was appointing new staff for the increased workload, she said.
''It will be a bit of extra work, but we will get it done.''
She met Manuherikia water users this week to discuss the recommendations, she said.
''We're giving some assurity. It will only be done if we walk with the whole community.''
The council will discuss the recommendations at an emergency meeting next week.
Mr Parker gave it until December 24 to respond.