Canterbury Regional Council chairman Sir Kerry Burke has been ousted by eight votes to six at a council session on Thursday.
Councillors who voted against Sir Kerry said that he had failed to unite the council and there was little confidence in his leadership both locally and nationally.
They said the vote was not about water rights or unitary authorities - issues the council has been divided over and on which Sir Kerry has expressed strong views.
His supporters said the "back room coup plotters" had behaved disgracefully and the leadership battle was all about water.
Sir Kerry said his ousting would leave a bitter an unstable council. He has been replaced by Alec Neill.
The resolution was moved by rural councillor Mike Oldfield and seconded by rural councillor Jo Kane.
Before the vote, Sir Kerry said disagreement over the council's handling of water rights was behind the letter and leadership vote, and said his ousting would leave a bitter and unstable council.
He rejected an accusation of a failure of leadership on water management and said he believed the council had succeeded in balancing a range of competing interests.
Ten Canterbury mayors had written to Local Government Minister Rodney Hide saying they have serious concerns about the council.
Sir Kerry said the mayors had been devious and should have brought their concerns to the council first.
In August, eight of the 14 councillors supported a vote of no-confidence in Sir Kerry Burke, claiming that he lacked leadership, credibility and was too focused on Christchurch.