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Dr Selva Selvarajah and Dr John Threlfall, who deal with the council's consent processes and environmental science, in particular concerning water quality and quantity, respectively, will leave within the next few weeks.
They are going through the redundancy process and said they were disappointed by the disestablishment of their roles but did not want to comment further.
Both had families and hoped to stay in Dunedin.
Mr Bodeker said he was not prepared to comment on the loss of the pair's jobs, commenting that, overall, the restructuring would add three extra staff to the organisation.
The restructuring was aimed at angling the organisation so it could successfully implement its water quality and quantity plan changes during the next six or seven years, he said.
The changes came into effect yesterday.
Under the restructuring, four directors' positions had been ''disestablished'' and replaced by two. A new stakeholders engagement directorate, which was being advertised externally, had been created.
The two ''new'' directorates combined the work of Drs Selvarajah, who had been with the council for 13 years, and Threlfall, who had been with the council nine years, with that of existing directors.
Fraser McRae will add the Resource Management Act work of Dr Selvarajah to his policy portfolio under a new title: director policy, planning and resource management.
Dr Gavin Palmer will take on Dr Threlfall's environmental information and science work alongside his existing hazards and engineering work as director engineering, natural hazards and science.
The only directorate to escape major changes was that of corporate services director Wayne Scott. Jeff Donaldson's regional services directorate was renamed environmental monitoring and operations.
The new stakeholders directorate would incorporate communications and community liaison activities previously included in Dr Threlfall's directorate and across other directorates.
Peter Taylor's associate directorate in strategic communications and education had been disestablished and his role was now communications manager.
Nicola McGrouther would lead the land resources team and the implementation of plan change 6A, while Marian Weaver, a resource management procedural specialist, would lead an equivalent team in implementing plan change 1C, he said.
Council chairman Stephen Woodhead said it was not appropriate to comment on what was the chief executive's decision.
''It is up to him to put a team in place to fulfil the council's objectives and work programmes.''