Southern Clams managing director Roger Belton said the past 22 months had been a long wait for the decision.
''We've had to shelve all our development plans and decline new market demands as we were limited to only harvesting from Blueskin Bay which is vulnerable to regular closures throughout the year,'' he said.
The decision had given the company a boost in confidence for a secure, productive and sustainable future, with prospects for development and a 25% staffing boost to 40 people.
Edward Ellison, Otakou runanga upoko and head of the Otakou hapu, was contacted and said ''it was not the outcome wanted''.
However, under the agreement to let commercial harvesting go ahead, the runanga and Southern Clams would work together.
''Monitoring will go on and we'll [together] develop a monitoring programme ... hopefully this will satisfy our concerns,'' Mr Ellison said.
Southern Clams general manager Dave Redshaw said rejuvenation monitoring was important, as some beds could be harvested annually, while others had to be left alone for two years.
More clams would initially be taken from the harbour so as give Blueskin Bay a respite from harvesting, he said.
Harvesting resumed last Thursday.
Under a special permit, between 2009-17 clam harvesting was permitted on two Otago harbour sand banks, equating to 4.5% of harbour area, so Southern Clams could scientifically evaluate the environmental effects of commercial clam harvesting.
Mr Belton said the research conclusion satisfied the Government commercial harvesting was likely to be sustainable with low and manageable environmental impact.
However, in 2009, other research by a University of Otago PhD marine science student was at odds with the finding, fuelling ill-feeling with the runanga.
''Now that we have diversity in our harvest areas, we can broaden our supply base and be more responsive to market needs,'' Mr Belton, who is overseas, said in a statement yesterday.
''It's very exciting for the company and for Dunedin. This is one local industry that is not going to relocate,'' he said.
Established in 1983, Southern Clams exports 80% of its harvest and the balance is for domestic markets, getting live cockles to restaurant tables around the world within 48 hours of harvest.
Mr Belton said having access to the harbour and Blueskin Bay provided more confidence in ensuring sustainable production and better management through rotational harvesting to meet demands.
Any closure of a harvest area could seriously affect Southern Clams' ability to deliver, he said.
Mr Belton said five years ago the company made plans and costings for product diversification and these would now be revived, which could result in the workforce growing from from 30 to 40.
''Now, the local clam resource, the largest of its kind in the country, can confidently contribute to sustained growth of the city's economy,'' he said.
Papanui Inlet had been reopened to clam harvesting for a year, albeit under a restriction that they be processed and not sold raw. Southern Clams pulled out of a plan to mature Bluff oysters in Dunedin's harbour, following the mid-2017 oyster parasite Bonamia ostreae outbreak on farmed oysters on Stewart Island.
simon.hartley@odt.co.nz