Port Otago received no advance notice or warning from Maersk before notification last Thursday it was withdrawing 104 ship calls from its Southern Star Service from September 1.
Container numbers were expected to drop from 225,000 to between 170,000 and 180,000, Port Otago chief executive Geoff Plunket said in a letter to staff obtained by the Otago Daily Times.
The decision affects mainly "trans-ship" container handling movements - where exports from other cities are routed through Port Chalmers.
Port Chalmers has been dropped from Maersk's transtasman Southern Star Service, which handled containers from the North Island exported via Port Chalmers.
Maersk has also opted to bypass the port and pick up containers railed to Christchurch at Lyttelton with the Southern Star Service.
The Maersk-Hamburg Sud alliance will add a ship call to Timaru for extra South Canterbury produce, but some of that produce will still be consolidated in Port Chalmers for export.
Mr Plunket said yesterday he was given about 24 hours' notice of the Maersk decision late last week.
Port Chalmers remained the principal South Island port and the changes would not impact directly on southern exports.
"We're still the South Island's preferred hub port," Mr Plunket said when contacted.
Maersk, the world's largest container shipping line, would continue to be Port Otago's biggest customer.
In December 2005, it chose Port Chalmers over Lyttelton for its main South Island port of call but shipping schedules can be changed without notice.
Mr Plunket said no jobs at Port Otago would be affected.
Recruitment would be curtailed and there was likely to be less overtime available to the existing 300 staff.
Container volumes since 2006 had increased 54%, from 135,000 a year to 209,000 during 2008.
The decline to about 175,000 containers "was still as good as our second best year", in 2007, when Port Otago handled 171,000.
Growth potential remained strong during the next three to five years because the dairying industry in the South, which had grown by 126% during the past five years, was increasing with more conversions.
Meat exportswere expected to make gains during the next three to five years, he said.
In his letter to staff, Mr Plunket said 2008 was a year of "unprecedented volatility".
Port Chalmers secretary of the Maritime Union of New Zealand, Phil Adams, said he was disappointed Maersk had made its decision to cut calls at Port Chalmers "on a whim", but remained positive.
Port Otago announced in August 2007 it wanted to undertake major dredging operations in Otago harbour to make it the South Island's only deep-water port, with the expectation deeper draught ships of up to 6000 TEU (20 foot equivalent containers) would begin calling in three to four years.
Mr Plunket said planning for dredging would "quietly go ahead" as the aim of attracting the major shipping lines remained a long-term strategy.
