Pupils at Valence Primary School in Dagenham, Kent - some as young as five - are only being allowed to drink water and dinner ladies are confiscating any juice.
But parents have complained that some of their children 'do not like water' and so go the whole day without quenching their thirsts.
Without wanting to be drawn into the row, the British Dental Association says that fruit juice should be given to children as an 'occasional treat' and ideally 'diluted' because it was 'highly acidic'.
In a letter to parents, headteacher Elizabeth Chaplin said the new rule was part of a campaign to win a London Healthy Schools Award.
She wrote: "As part of the school's action plan it was decided that our first step would be to ensure equality for all the children and that everyone would be offered water to drink at lunch time.
"You will no longer have the worry about providing a drink as we will supply the water.
"Please do not put any drink other than water in your child's packed lunch box as they will not be able to drink it at school."
But some angry parents said children who do not like water are being forced to go the whole six-hour school day without a drink.
Carly Nunn, 26, claimed her five-year-old daughter, Teagan, had her drinks taken away by a dinner lady.
She said: "She put a straw in the carton and took one sip and it was taken off her and put in the bin.
"The next day, I put it in a bottle, but it was tipped onto the table to check the colour."
Ricky Biggs, 31, has kept his son Ronnie, four, off school because of the ban.
He said: "He doesn't drink water and when he's been in hospital they've given him squash. How can a hospital say squash is healthy, but a school say it isn't?
"We spoke to the head about it and she just offered us a transfer form."
Ronnie's mother, Kelly Debenam, added: "The letter makes it sound like they're doing the parents a favour, but they're not.
"Other schools don't have this, it's not compulsory, it's just them trying to get this award."
Head Mrs Chaplin said children questioned over their drinks were 'more than happy to confirm or demonstrate the water content'.
She said: "Regrettably our attempts to promote a healthier lifestyle have been received negatively by a very small minority.
"We are undertaking a review of the whole lunchtime provision and the review group will include representatives from the parents, pupils, staff and governors."
The London Healthy Schools Award scheme grades schools bronze, silver or gold for improvements made to pupils' health.
The British Dental Association's scientific adviser, Professor Damien Walmsley said: "Despite the huge improvements in children's teeth in the past 40 years, there still too many areas where children experience high levels of tooth decay caused by frequent snacking on sugary foods and drinks.
"Although fruit juice is a natural product it is packed with sugar – at similar levels to well-known brands of cola – which increases the risk of tooth decay.
"Besides sugar, parents may be unaware that fruit juices are often highly acidic, which can erode the surface of teeth, making tooth decay more likely.
"If you must drink fruit juice it best taken as an occasional treat, diluted and at mealtimes but it would be far better to eat the fruit and have water to drink."
THE HEAD'S LETTER IN FULL
"Dear Mums, Dads and Carers
Happy New Year! I hope you all had an enjoyable Christmas break and that you are prepared for a very eventful year ahead whatever the weather.
I just wanted to ensure the message that went home in the December newsletter regarding drinks with packed lunches was read by all parents.
We have always promoted and encouraged our children to adopt healthy lifestyles. We held the healthy schools award for many years. The government and the Mayor of London are urging all schools to take the lead in reinforcing the benefits of eating and drinking healthily.
They are going as far as providing the funding for all children in reception, year one and year two to have free school meals from September if parents wish to take up this offer.
Our school dinner menu is nutritionally balanced and the only drink available to the children is water.
As part of our application for the London Healthy Schools Award, we have been asked to consider how we are reinforcing the message for those children who bring in a packed lunch from home.
As part of the school's action plan it was decided that our first step would be to ensure equality for all the children and that everyone would be offered water to drink at lunch time.
You will no longer have the worry about providing a drink as we will supply the water. Please do not put any drink other than water in your child's packed lunch box as they will not be able to drink it at school.
In addition, we are recycling all our food waste from the kitchen and school dinners and are paying for this service.
In order for you to check what your child has eaten and to reduce our recycling we are sending all the waste from packed lunches home.
All children have access to water at all times throughout the day and we encourage children to drink regularly.
A healthy child is a happy child and we hope that by working together we can achieve our aims.
Thank you for your continued support.
Mrs Chaplin Headteacher"
• What do you think? Is the Head right to ban fruit juice? Do some children really not like water?
More on Parentdish: The worst sugary drinks for children revealed - some surprises here.