Southern Clams was awarded a special permit in July, allowing the Dunedin-based fishing company to carry out research trials on commercial cockle fishing in the middle banks of the harbour for three years.
The company's purpose-built barge, Tuaki, returned to Dunedin with four tonnes of cockles yesterday, raising the ire of Otakou runanga tangata tiaki/kaitiaki (customary manager) Hoani Langsbury.
"We are shocked commercial harvesting is happening under the guise of research. It is akin to how they do Japanese whaling."
Mr Langsbury, one of the organisers behind a mataitai for Otago Harbour, said the harbour had been closed to commercial harvesting for more than three decades and he was disappointed to see cockles taken from the area.
While the mataitai - if approved - would exclude commercial fishing, Southern Clams would still be permitted to fish in the designated area as part of its research permit.
Catch taken under the research permit was allowed to be exported overseas.
Mr Langsbury said the runanga had approached the Ministry of Fisheries to revoke the research permit, but that was unsuccessful.
Southern Clams operations manager David Redshaw said the company was pleased with yesterday's harvest.
Seven people using body dredges harvested a total of four tonnes of cockles in just over an hour, he said.
Under the permit, the company could take 650 tonnes of cockles a year from Otago Harbour for three years, with a possibility of a two-year extension.
The permit would enable research to be carried out on the sustainability of the harvest.
The quality of the cockles was similar to those harvested from Blueskin Bay and was a "niche" product, Mr Redshaw said.
The majority of the catch would be exported to the United States and then to some Asian markets, with 20% for the domestic market, he said.
