The ruling could help bring an end to an ongoing global dispute over the safety and nutrition benefits of the two rival milk formulations, following calls that products containing the proteins should be labelled with health warnings.
The decision, reflects the increased pressure on processors to ensure health claims attributed to their products can be substantiated.
According to Australia-based A2 Corporation there are two different main forms of beta casein, which account for 80 per cent of the proteins that make up cow's milk.
These are the A1 and A2 proteins.
The A1 beta casein differs from A2 by just one amino acid.
The company claims that international studies have linked the A2 protein to a reduction of health risks, compared to A1.
In the NZFSA ruling food standards director Carole Inkster said that arguments suggesting that A1 or A2 milk offered sufficient health benefits over each other were unjustified.
The ruling was in part based on a 2004 peer reviewed study, She added that claims that both the proteins could also pose a food safety issue had also yet to be substantiated.
"Recent media reports of issues with milk are not backed by scientific evidence," Inkster stated.
The claims are linked to the findings by Professor Boyd Swinburn's 2004 report on the potential benefits of A2 milk over the A1 variety.
The report focused on claims made by the A2 Corporation claims milk containing A1 could trigger heart disease, autism and some types of diabetes.
Its A2 milk contains only the A2 variety of beta casein protein.
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.
The company was alleged to have suppressed research-linking milk containing the A1 protein to autism, schizophrenia, diabetes and heart disease.
Though Swinburn's did not rule out a possible link between A1 and some diseases in his report, he called for further study, backed by "good human trials" before a verdict could be made.
Though the report 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.
Despite this need for further testing, Inkster added that a lack of current international reaction to the debate had led to decide there were minimal dangers concerning milk protein use.
"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," she stated.
A2 milk was launched in New Zealand and Australia in 2003 and has also seen some interest in the UK.
The product derives its name from the type of protein contained in the milk.
Most of the milk sold in the UK contains more A1, which some researchers have claimed could increase the risk of heart disease.
Some scientists have suggested that high rates of cardiovascular disease in certain regions of the UK could be connected to the type of milk produced in those areas.