It is still unclear exactly how many jobs will go, but at least 23 workers have taken voluntary redundancy and out of 16 staff who could have been forced into redundancy, many have been offered jobs in other parts of the operation.
The issue of forced redundancy had threatened to spill over into industrial action, but following a meeting of 150 cargo handlers on Thursday and "eleventh hour" talks with Port Otago, both parties agreed there would be no forced redundancies.
The redundancies were prompted by an expected 40,000 container, $4 million shortfall across Port Chalmers' wharves this year.
Union national president and Port Chalmers secretary Phil Adams said while the port was already receiving one fewer ship visit per week, cargo volumes were still higher than expected, surprising staff and management.
"Things looked pretty bleak when the redundancies were first announced," Mr Adams said.
Port Otago chief executive Geoff Plunket was "very pleased" not to be making any forced redundancies.
He confirmed higher than expected cargo volumes and staff re-deployment had been the saving grace for about 12 positions.
Port Otago has been free of outright industrial action for more than 20 years and Mr Adams said he was pleased "not to get into an industrial dispute".
The outcome was "win-win", with reduced job losses for staff and productivity maintained.for the company.
"It's a difficult economic period, but the port has weathered difficult times before and we are confident we will this time as well," Mr Adams said.