Maersk Dunafare arrived at Port Chalmers at 2pm on Thursday and was to have left at 3pm yesterday, but the latest information provided on Port Otago's website listed the ship as expected to depart early this morning.
Union officials said port management had to call a third shift to complete loading because of go-slow action by workers, which meant the ship missed its scheduled sailing time.
Port Otago chief executive Geoff Plunket declined to comment.
Maritime Union of New Zealand Port Chalmers secretary and national president Phil Adams said while his union was in dispute with the port company over the introduction of the new flexible shift, it had not authorised any industrial action.
"It certainly has not been organised by the union. I think there is a bit of anger out there," he said.
Mr Adams said loading had been slow as workers were being "very careful".
Health and safety concerns with the proposed flexible shift could result in the issue being taken to court.
Mr Adams said that was an option being considered by the union, which had concerns about the impact on workers of neither knowing when they would have work nor for how long.
Port Otago has said 35 people would lose their jobs after restructuring of its workforce to cope with a 15% downturn in container volume, and has called for voluntary redundancies.
