The decision by Dr Rob Lieffering, Sharon McGarry and Philip Milne was released today.
Reasons included the potential for "some overflows to have short lived but significant adverse effects on the environment’’.
In April the Queenstown Lakes District Council applied for a 35-year permit to discharge from its wastewater network when blockages, breakages, system failures, extreme storm events, and over-capacity in the council's network of pipelines occurred.
Freshwater bodies affected include Lakes Wakatipu, Wanaka, Hawea and Hayes, the Kawarau, Shotover, Clutha, Hawea, Cardrona and Arrow rivers and Luggate Creek.
Commissioners said it had insufficient evidence to be able to determine the extent of adverse effects from future overflows.
The application had little support from the objectives and policies of both the statutory and non-statutory planning documents it was being tested under, they said.
Their decision matched that of Otago Regional Coucnil principal consents officer Peter Christophers and senior consents officer Charles Horrell, who wrote the application was "overwhelmingly inconsistent with all relevant planning documents’’.
The regional council received 200 submissions in relation to the application, of which 197 were opposed, one which was neutral and two which were in support.
The district council’s counsel Janette Campbell told the commissioners at the hearing such a consent was the "responsible and transparent option'' for managing overflows, and would give the regional council a greater level of scrutiny than it had now.
It had an "ambitious'' 10-year programme of investment to improve the network's resilience, and was proposing an ongoing public awareness programme to prevent blockages from entering it in the first place, she said.
The decision is subject to appeals until January 31.
The regional council said it would not comment during the appeals period.
The Queenstown-Lakes District Council has been approached for comment.
