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The ship Xin Zhang Zhou will stop at Port Otago for the last time on June 3 and will then finish its visits to the country in Wellington.
It was one of four partners of the "Anzac" service which travelled down the coast of New Zealand and back to China.
Port Otago chief executive Kevin Winders said it was "disappointing" to lose the ship from the port.
"It’s been a marginal service for a number of years and been reviewed every February," he said.
"The economics of the call has always been in question and obviously the Covid issue and disruption in China was the final straw."
He said most shipping lines around the world were struggling financially and were looking for ways to improve efficiency and save money.
The products that were shipped on Xin Zhang Zhou would likely end up with one of the other providers visiting Port Chalmers, Mr Winders said.
Work was being carried out to ensure that happened.
Business in general for Port Otago was steady despite the difficulties posed by Alert Levels 4 and 3, Mr Winders said.
Volumes were steady, including log volumes which were returning to previous numbers.