Normally, the council would establish its own hearings panel but it decided this week to ask Environment Minister David Parker to wade in and take the matter immediately to the environment court or a board of inquiry.
Council chairwoman Marian Hobbs said the so-called ministerial "call-in" could help to cut costs and speed up the process.
"The standard process for a plan change can take years to complete, assuming there are appeals to the environment court and beyond. Having a plan change called in by the minister restricts appeals to the high court on points of law, while still allowing the community to make submissions and speak at hearings."
The water permits and water quality plan changes were necessary interim steps as the council worked to confirm a new land and water regional plan for Otago by the end of 2023, she said.
The water permits plan change, recommended by Mr Parker following a review late last year, creates a resource consent process for the short term to manage expiring water permits and historic water permits granted for gold mining, while a new planning framework is developed.
The water quality plan change would target, among other things, sediment runoff from new subdivisions or developments, farm effluent management and good management practices to meet government expectations.
Not everyone was pleased with Wednesday’s decision. The council was divided on the matter and late on Wednesday Federated Farmers said the move "cuts out crucial community input and robs us of the opportunity for decisions that reflect local knowledge and a local voice".
Council chief executive Sarah Gardner told councillors that advice she received from the Auditor-general’s office indicated councillors could vote on Wednesday’s decision.
Nevertheless, Cr Andrew Noone abstained on the water quality plan change vote.
Before the vote, several councillors suggested they were blindsided by the inclusion on the agenda of the report, which initially indicated a preference for a board of inquiry rather than the environment court.
After the meeting Cr Gary Kelliher, among the five councillors who voted against the ministerial call-in, said he was "uncomfortable" with the process.
The added "extra detail" to the water permits plan change was a sticking point in the community, and the council could "jeopardise community input into the big plan change [the land and water regional plan]".
During the meeting, Ms Hobbs said the focus of the council ought to be on the coming land and water regional plan.
"We need to get these comparative minnows out of the road relatively quickly," she said.
Cr Alexa Forbes said she liked the idea of taking the interim water management rules to a higher authority.
"The heat comes out — it makes it more independent," she said.
