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The port company's wage bill for its year to June rose from $30.6million last year to $32million, and the company currently has 329 staff, of which 72 are paid more than $100,000.
Port Otago chief executive Kevin Winders said many of the 24 staff at the bottom of that range, $100,000-$110,000, were cargo workers, including operators and heavy machinery drivers.
He said shift work, penal rates and superannuation all contributed to the more than $100,000 each earned.
The top three earners, unnamed, were paid in scales of $500,000-$510,000, $380,000-$390,000 and $290,000-$300,000.
Remuneration included salary, bonuses and motor vehicles.
Port manager Peter Brown resigned unexpectedly in late March after 11 years with Port Otago.
No employee is named on the remuneration scale, but only one is noted as having left during the financial year, having been on $270,000-$280,000 scale.
It was noted that employee's ''normal levels of remuneration were exceeded''.
Mr Winders was asked what the ''exceeded'' remuneration level payment was for.
He said it was the former employee's holiday entitlements at the time, and when asked, he confirmed no other payments were made.
Port Otago's directors were paid a total of $327,000 for the year, each having roles with the port company and also its subsidiary Chalmers Properties, costing in total $243,000 and $84,000, respectively.