In a statement, they said they made errors in the calculation of the amounts of EPA and DHA in five of the fish oil supplement capsules, "which means that we have underestimated the doses".
"All are now within 15 per cent of label value. This, in turn, affects our assessment of compliance with health claims; however, they remain variable."
In a statement released today, the journal and study authors unreservedly apologised to the manufacturers, suppliers and the public for the error.
"Errors occur in research publications from time to time and it is very important to put the scientific record straight as fast and accurately as possible," journal editor Frank Frizelle said.
"This happens often enough that there are well established scientific guidelines around the process of how this is undertaken, written by the International Committee of Medical Journal Editors (ICMJE) that the NZMJ adheres to.
"When an error is minor, that is it doesn't alter the main outcome of the study, then then this is dealt with by an erratum.
"When an error is major, that is the main conclusions of a manuscript are invalid, then the manuscript must be retracted, as we have done."
Natural Health Products NZ (NHPNZ) contested that the study was flawed because the tested fish oil products had different capsule sizes.
Some capsules were 1 gram, some were 1.5 grams and others were 2 grams.
When the laboratory analysed these capsules, in keeping with its normal testing practises, it stated all results in terms of the amount of omega-3 per gram.
NHPNZ argued that, when calculating the quantity of active ingredient in each capsule, the researchers failed to take account of the fact that the test results were in one gram units, so should therefore have been extrapolated for larger capsule sizes.
"When assessing the label claims for products with 1.5 gram capsules, the researchers did not multiply the test results by 1.5 to give an accurate result," the group stated.
"Correctly extrapolating the test results for each capsule size has identified that all but one of the tested products were well within acceptable tolerances related to their label claims."
The group's chair, Lorraine Moser, said the paper had presented "label claim inaccuracy fiction as fact, needlessly damaging the industry's reputation and needlessly giving consumers cause for concern".
The group has also alleged there were other flaws with the paper.
The study followed others that had contested the accuracy of fish oil labels.
Four years ago, scientists from the University of Auckland's Liggins Institute tested 36 brands and found just three contained the same concentrations of omega-3 fatty acids as listed on the label.
Their analysis revealed that the products contained an average of just 68 per cent of the claimed content - and more than two thirds of supplements tested contained less than 67 per cent.
Two products included only a third of what was on the label.
Since then, an international systematic review, drawing on nearly 80 randomised trials involving more than 100,000 people, suggested long-chain omega-3 supplements like fish oil did little to protect against heart attack or stroke.
There have also been positive findings, with Liggins researchers also showing that fresh fish oil may prevent children of overweight pregnant women from later developing diabetes.
• The Herald's original article on the study has been modified to reflect the retraction.
