The 95-page "Sanitary Survey Report", written by Nelson-Marlborough animal products officer Jeremy Shearer, concludes that the harbour's water has levels of contamination low enough for cockles to be safely harvested at most times.
Southern Clams director Roger Belton hailed the Dunedin City Council for its efforts in reducing discharges into the harbour.
He considered the 27-month, $52,000 survey was "a huge endorsement" of the work done over the last nine years in removing all outfalls of sewage and improving the quality of wastewater being discharged into the harbour.
"Otago Harbour would now be one of the cleaner inshore shellfish growing areas in the country," he said.
The report states that two cockle beds it labels 1804 and 1805 [see map], meet New Zealand and European Union standards for harvesting, except on occasions when there are high inflows of water from such tributaries as the Leith River and city stormwater drains.
"The only times regulatory limits are expected to be exceeded are after very heavy rainfalls," Mr Belton said.
The harvest of "bivalve molluscan shellfish" such as cockles (known as clams in America) is subject to the Animal Products Regulations 2006.
Southern Clams, which exports cockles from Blueskin Bay, near Waitati, has applied for a "special research permit" to allow five years of research into the commercialisation of Otago Harbour cockle beds.
The report notes that before 2000, sewage from about 6000 people was still going into the harbour.
"It is only relatively recently that sewage discharges into the harbour have ceased and farming of shellfish . . . can be contemplated."
Mr Shearer found that, apart from small communities such as Aramoana, Harwood and Otakou still using septic tanks, the only actual sewage in the harbour came from boats moored at the Dunedin boat harbour and around Port Chalmers.
He estimated that, on average, this would be from a total of only four people per day.
Mr Shearer's survey looked at the possible sources of water contamination along the 22km length of the harbour.
He concluded, in part, that:
•There were "minimal" concerns over cadmium and fluoride discharges from the Ravensdown Fertiliser Co-operative.
"This industry has only very localised impacts on the sediments and biota of the harbour."
•Three dairy farms in harbour catchments were "small scale", with fewer than 400 cows in total.
•"Under most circumstances. . . a very small proportion" of the daily faecal coliform production from 10,000 sheep, 900 cattle, 150 goats, 50 pigs, 10 deer and 15,000 possums would enter the harbour.
•Seabirds gorging on dense swarms of krill "pose a threat" to seawater and shellfish quality, and this would need to be accommodated in cockle harvesting criteria.
•Ships calling at Port Otago "are expected" to exchange ballast water in mid-ocean.
•Ships were also "obliged to honour" a no-discharge sewage policy while in the harbour.
•Stormwater from urban areas contained "high levels" of sediment, bacteria and heavy metals, which had an impact on the cockles, "but these impacts are of short duration in both areas and very limited in area 1804".
•A "guarded conclusion" on the effects of contamination from the Leith Stream was that "any influence of these discharges will be of limited impact and duration".
Flows in the stream would be used as a "predictor" of increased pollution levels in the harbour, brought about by rainfall.
With the completion of the survey, the New Zealand Food Safety Authority is expected to declare the cockles meet shellfish food safety standards.
Communications manager, Gary Bowering, said that the report showed "the waters were fine", subject to certain management systems being in place.
"Basically, the harbour is clean enough to support the [cockle] industry."
Mr Belton said the survey, along with another, already completed, showing the size of the resource, were the two prerequisites required by the Ministry of Fisheries before a commercial fishery could be established.
The Ministry is processing an application from Te Runanga o Otakou for a "mataitai" reserve covering most of Otago Harbour, which would prohibit commercial exploitation of the cockle beds.
A Ministry spokesman said yesterday 41 submissions had been received from individuals and the next step in the process would be a public meeting, probably at the University of Otago, in mid-February.
Following that, commercial fishing interests would be invited to make their submissions.
