It's a voluntary system with most pure fruit juices getting between four and the maximum five stars.
But a meeting last Friday the Australian and New Zealand Ministerial Forum on Food Regulation opted for a new system rating pure fruit and vegetable juices on their individual sugar content.
Professor of Population Nutrition at Auckland University Cliona Ni Mhurchu said fruit juices that have a naturally lower sugar content like lemon juice, will still get four stars.
"Orange juice, which is probably the most commonly consumed juice, will still rate between three and three-and-a-half stars. It's really those juices that are particularly high in sugar and very sweet like apple and pear juices that will rank the lowest in terms of stars. They would probably get between one and one and a half stars," she said.
Professor Ni Mhurchu said the idea was to encourage shoppers to choose the healthier option.
But Katherine Rich from the Food and Grocery Council was questioning the decision.
She said water would get a poor rating under the system because while it doesn't have any sugar, salt or fat in it neither does it have any nutrients - yet it was given the top score of five.
"And that was just a policy decision because water, if you put it through the health star rating would actually get a much lower rating. And so ministers determined in that instance, that if it got a lower rating that would send the wrong message to consumers. So that's why they've given it an automatic rating of five," she said.
She said the ministers should apply the same discretion to pure fruit juice.
The decision has also drawn strong opposition across the Tasman with the growers' industry group Citrus Australia saying it's shocked and disappointed.
It objects to a system where diet coke ends with a higher health rating than fresh juice.
In a statement, its chief executive Nathan Hancock said state governments have lost their way.
"Despite evidence that fresh juice contains nutrients vital to physical and mental wellbeing, these governments have deferred to the anti-sugar lobby, which has had fresh juice in its sights since the health star rating system was formed. Governments have missed a chance to encourage consumption of fruit and vegetables in the form of juice. Choosing to cave to the anti-sugar brigade against all logic," the statement said.
Professor Ni Mhurchu said drinking water is still the healthiest option and it's better to eat fruit whole, rather than juice it.
She said she understood people could find the comparison with diet soft drinks confusing.
Because diet drinks don't actually contain sugar, then they can rank higher than some fruit juices. But at the moment it was decided that it was better to give consumers some low sugar options including diet drinks and also to give manufacturers an opportunity to reformulate their products if they want to reduce the sugar content.
But Rich said the producers can't reformulate fruit juice because it's a natural product.
She said consumers would find the ratings confusing, potentially bringing the scheme into disrepute.
"It's up to ministers to make the decision based on the science and I would hope that science and common sense trumps ideology, but the issue is that they're the ones who have to explain to consumers why there's a discrepancy between diet drinks or soft drinks and a natural fruit juice," she said.
The minister responsible for food safety, Dr Ayesha Verrall said the change is the result of an independent robust review.
She said while fruit contains many beneficial vitamins and nutrients, it's the overall amount of sugar in juices that causes diabetes and tooth decay.
Manufacturers have two years to implement the changes, although the system remains voluntary.
