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Port Otago chief executive Kevin Winders said there had been "several complaints" since the arrival of the Rio-class ships used by shipping giant Maersk - one of the six sister ships now visits every weekend - on rotation.
"Depending on your elevation, you really feel a thumping sound from the generators," Mr Winders said.
Maersk's smaller, L-class vessels have been phased out in preferance to the Rio-class, which can carry up to 5200 TEUs (20 foot equivalent units), as opposed to 4500, the maiden call having been in late-October.
They carry a larger percentage of refrigerated containers, between 1800 and 2000, of the total 5200 TEUs aboard and require more energy.
The Rio-ships use the two large generators to keep the refrigerated containers cold; the 11MW of power needed being the equivalent of that used for 750 homes.
Mr Winders said "plugging into the national grid" was not an option without major infrastructure upgrades, starting with services in Dunedin city.
In a community paper message to Port Chalmers' households, Mr Winders said he was both "surprised and disappointed" with the noisier Rio-class ships, given they were a decade newer than their predecessors.
"We hoped the first one was the exception, but as each new [Rio] ship arrived they were similar to the first Rio," he said.
A starting point for noise mitigation was to berth the vessels further up the wharf, with their sterns facing landward, towards Port Chalmers.
"Please bear with us as we work through this period," he said.
He said still or northerly winds during summer had not helped the problem, and expected a return to southerlies to change the noise impact.
Another shipping line's vessel, CGM Coral had to be berthed bow-on to Port Chalmers last week, because its port-side gangway was broken.
Mr Winders said while it was noisy for people in Careys Bay, he hoped the way it had to be berthed would be an exception.