It is the third shipping operator to reduce southern services during the past 11 months.
The loss of the service, run by Maersk, MOL and NYK and Hamburg Sud, means Otago importers and exporters, mainly in the horticulture and meat sectors, will have to use road/rail transport between Otago and Canterbury if other means of shipping are not available.
Port Otago is about to announce a record year in 2008-09 for container volumes.
Port Otago chief executive Geoff Plunket said he was "disappointed" with any service loss, but said domestic New Zealand services and other shipping would be available to Otago exporters, including "slot sharing", where competing shipping lines had space allocated on rivals' ships.
He said the fortnightly service to Japan and Korea had not changed in recent years, but change was anticipated.
He highlighted that, globally, shipping services were being reduced in line with falling cargo volumes.
"There have been huge [service] changes in the past two years. All ports have been affected. We're not affected any more than most," Mr Plunket said yesterday.
There were thousands of ships laid up across the world as shipping lines vied for dwindling cargo volumes amid the worldwide recession.
Otago Chamber of Commerce chief executive John Christie said the time and money spent by Otago exporters and importers finding a new service would increase overall costs and further squeeze profit margins.
"The reality is the shipping industry, which is a costly and complex sector, is going through upheaval and it's the rationalisation [of services] we're seeing," he said.
Mr Plunket said there was no forecast for 2009-10 container numbers through Port Chalmers and it was "too early to quantify" how the loss of Hamburg Sud would affect numbers.
In an announcement obtained by the Otago Daily Times, the ICS/Cosco consortium of shipping lines Maersk, MOL and NYK and Hamburg Sud said that, due to the global downturn in trade, they had decided to reduce capacity in the trade between northeast Asia and New Zealand under a "rationalisation" process.
While not mentioning the cancellation of the Port Chalmers service, the announcement said the new service would call at Tokyo, Kobe, Busan, Shanghai, Yantian, Hong Kong, Auckland New Plymouth, Nelson or Wellington, Lyttelton, Napier, Tauranga and Tokyo.
"Other origins in New Zealand will be covered by feeder options."
In August last year, Maersk, Port Otago's largest customer, announced it was cancelling 104 ship calls from September.
That was followed a month later by Hapag Lloyd quitting its weekly call to Port Chalmers.
Container volumes at Port Chalmers had risen 54% since 2006, from 135,000 to 171,000 in 2007, and to 209,000 during 2008, but Maersk's withdrawal was expected to remove 45,000-55,000 containers off annual volumes this year.
However, Mr Plunket said despite an earlier forecast downturn to 180,000 containers for the year to June, Port Otago was now expected to report a record 215,000-220,000 for the year, due to a "strong" export season across all export types.
In early-November, Dunedin-owned Pacifica Shipping resumed a domestic shipping service out of Port Chalmers - having departed in 2005 - linking with Lyttelton, Tauranga and Auckland.
Pacifica wanted to trans-ship about 1000 containers around the coast each week for the 130m Spirit of Endurance.
The new northeast Asian service, of six ships operated by four shipping lines, had committed to providing additional capacity for peak-season New Zealand exports, with all six ships having 500 refrigerated container plugs.
