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Port Otago chief executive Kevin Winders confirmed yesterday Mr Brown had resigned last Thursday.
He said the resignation was ''unexpected'' and could give no reason for his departure, other than it was Mr Brown's decision.
Mr Winders said the commercial manager position had since been advertised nationally.
Mr Brown told the Otago Daily Times he had decided to move on after 11 years and would now ''challenge myself by
trying something different.''
He said he had enjoyed his time at Port Otago and felt privileged to have played a small part in the port company's success.
Mr Brown had been Port Otago's commercial general manager since 2007.
He had previously been with the Dunedin City Council's economic development unit for many years and was a former director of Dunedin Venues Management Ltd.