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Council stakeholder engagement director Sian Sutton has confirmed she resigned last week.
The Otago Daily Times has also heard from several sources that council environmental monitoring and operations director Scott MacLean is leaving the organisation.
The council said Mr MacLean was on leave and he did not respond to a request for comment yesterday.
They are two of six department heads who answer to chief executive Sarah Gardner.
Mrs Gardner declined to confirm or deny either departure.
''Basically we don't make any comment on personal staff matters.''
Councillors were contacted about the issue yesterday. Two replied.
Council chairman Stephen Woodhead said he did not comment on personal staff matters as they had a right to privacy.
Cr Michael Laws said Mr Woodhead should provide an explanation on behalf of the governance team as the council was a ''publicly accountable organisation''.
Ms Sutton said she would take up a new role in Dunedin but could not yet talk about it because she was still in negotiations.
''I've been in local government for a long time, but wanted to try something different,'' she said.
She heads the department dealing with public communications.
She moved from Australia for the role in August last year.
Under her, the council advertised eight new jobs in that department in September, which was part of revamping communication systems she said were ''not fit for purpose''.
Mr MacLean heads the team whose responsibilities include environmental inspections, the harbourmaster, biosecurity and consents.
He started the job in September 2015, promoted from his previous role as operations manager in the department.