Local Government Minister Rodney Hide has quashed plans by the Franklin and Papakura district councils to break away from the Auckland Super City.
Mr Hide has written to the councils, rejecting applications made late last year for each to become a unitary authority outside the Super City.
In a letter to Franklin Mayor Mark Ball, Mr Hide said he firmly believed the re-organisation of Auckland's eight councils into one council would strengthen the region's governance and result in cost savings for ratepayers and benefits to Auckland's communities.
Mr Hide has never said what cost-savings ratepayers could expect from the biggest shake-up of local government since 1989.
The minister has also written to Papakura Mayor Calum Penrose saying he did not support the council's bid to become a unitary authority.
Under the Super City, Franklin will largely be split in two between Auckland and Waikato, with a small area joining the Hauraki District Council.
The part of Franklin in Auckland will have its own local board with nine members.
Papakura will be fully absorbed into the Super City with a five-member local board.
Mr Ball said he was extremely disappointed by the minister's "blatant disregard of the wishes of the vast majority of people in Franklin".
He said residents had consistently opposed the re-organisation of the district in submissions, public meetings, a poll run by local media and three telephone polls.
Other methods of becoming a unitary authority - support from the Auckland and Waikato district councils or a petition in the two regional council areas requiring 186,000 signatures - were not achievable and would not be pursued, Mr Ball said.
A spokesman for the group Franklin.4.Democracy, who did not want to be named, said the decision to go against the wishes of the community could have "unintended consequences" for the National Party.
He said that the time before next year's general election would be filled by political and public discontent with the implementation of the Super City, and could lead to an independent candidate challenging the National MP for Hunua, Paul Hutchinson.