Vanessa Chan, the former general manager of Ashfield Council, was appointed above the former Leichhardt chief Peter Head and Marrickville general manager Brian Barret to the top position of the merged entity.

But staff were told on Friday that Ms Chan would be leaving the council, while Mr Head and Mr Barrett, who were appointed to deputy positions, left soon after amalgamation.

Multiple senior staff from the three former councils said it had been a difficult process of merger at the new organisation, which was now suffering from a lack of experience.

"Things haven't been going well," said one well-regarded executive. "It's classic collateral damage from a government process."

Former councillors on the three councils, who have been agitating for the government to hold elections for the new entity before September 2017, seized on Ms Chan's departure as evidence of mismanagement.

"Mike Baird promised amalgamation would deliver better services but instead basic services and proper administration are falling apart," said former Leichhardt mayor Darcy Byrne.

Former Greens councillor Max Phillips said: "Under the Administrator the new council is quickly spiralling out of control. The state government should schedule a March 2017 election so that the community can have confidence that their council is under control and direction."

Another former Leichhardt councillor, John Stamolis, said council committees had been dismissed, council business was in hiatus, and the costs of redundancies and rebranding were running into the millions.

"This is a dreadful experience to say the least and the Baird Government should be responding to it," Mr Stamolis said.

Staff were told on Friday that Ms Chan had resigned for "personal reasons".

In a statement the administrator of the council, Richard Pearson, said a number of staff "have left the organisation through a process of natural attrition that was inevitable when three sets of senior staff were merged into one organisation.

"The great majority of our management is still in place across the Council and their corporate knowledge, along with the mass of knowledge of the general staff, is still in place," said Mr Pearson, who has endured some torrid community relations since taking the position.

Keith Rhoades, the president of Local Government NSW, said there had been teething problems at a number of merged councils across the state. And another former Inner West Council executive, speaking on condition of anonymity, said many of the well-regarded staff at the council had opted to take voluntary redundancies knowing they would be able to find other jobs.