The authority yesterday announced that it has commissioned an independent review on the science behind health claims relating to the use of the A1 and A2 protein.
Results from the review could have major implications for milk and dairy product formulation across the globe, with major processors including Fonterra involved in the dispute.
A1 and A2 proteins are the two different main forms of beta casein, and account for 80 per cent of the proteins that make up cow's milk.
Just last month, NZFSA affirmed its position on the safety of the milk proteins, following intense media attention surrounding claims made in a recent book by Lincoln University professor Keith Woodford that the A1 protein may be damaging to health.
NZFSA acting chief executive Andrew McKenzie yesterday said the decision to further review the proteins was designed to allay consumer fears that there may be a danger in drinking the country's milk due to ongoing media coverage.
"We want to assure all New Zealanders that our role is to protect consumers and promote public health," he stated.
"The decisions that we make in order to do that are based on sound, scientific evidence and common sense."
The regulatory agency's original decision was based on findings from a 2004 report by nutrition expert Professor Boyd Swinburn on the potential benefits of A2 milk over the A1 variety.
The report focused on claims made by the A2 Corporation, which produces milk containing A2, that milk containing A1 could trigger heart disease, autism and some types of diabetes.
McKenzie stressed that NZFSA's decision to call for a review in no way weakens its current opinion that the country's milk is safe for consumers no matter which variety they choose to drink, but is vital in quelling rumours regarding the proteins.
The independent expert assigned to carry out the task will review the original scientific opinion available to NZFSA in 2004, while also looking at findings published since the original decision.
According to A2 Corporation, the A1 beta casein differs from A2 by just one amino acid.
The company claims that international studies have linked the A2 protein in its milk to an improved reduction in health risks, which it says is not the case with A1.
The alleged link between A1 milk and heart disease has caused much debate in New Zealand, leading to a court battle with major dairy group Fonterra, which supplies milk containing A1.
The company was alleged to have suppressed research linking milk containing the A1 protein to autism, schizophrenia, diabetes and heart disease.
Though Swinburn's 2004 reoprt did not rule out a possible link between A1 and some diseases, it called for further study, backed by "good human trials" before a verdict could be made.
However, NZFSA's food standards director Carole Inkster last month stated that "we are not aware of any new research from anywhere in the world, and can only conclude that the world's medical researchers have not seen the A2 hypothesis as a high priority for investigation".
A2 milk was launched in New Zealand and Australia in 2003, and has also seen some interest in the UK.
Most of the milk sold in the UK contains A1, leading some scientists to suggest that high rates of cardiovascular disease in certain regions of the UK could be connected to the type of milk produced in those areas.