David Moore, the HMI responsible for discipline issues, told a conference of Catholic secondaries that schools which limited the amount of carbonated drinks drunk by their pupils had noticed a marked improvement in behaviour.
He suggested that children needed to be taught the importance of drinking plenty of water to prevent dehydration. He called for every school to install water-dispensing facilities.
Mr Moore said: "Every school that has removed vending machines selling fizzy drinks or monitored consumption has noticed a real difference in the kids.
"I would not go so far as to say they should all be ripped out. It is more important to educate children of the effects these drinks can have and the importance of drinking lots of water and healthier drinks too."
Since Wolsey junior school in New Addington, south London, decided to stop selling fizzy drinks and other junk food four years ago, both the academic performance and bhaviour of its pupils has increased dramatically.
Headteacher Peter Winder said: "The change in the behaviour and concentration of the children was dramatic.
"Teachers now have to spend only around 15 minutes a day coping with poor behaviour instead of around two hours before the policy was introduced."
Another school to notice an improvement in behaviour since giving certain fizzy drinks the thumbs-down is Seaford College in Petworth, West Sussex.
Headteacher Toby Mullins said: "In September our tuckshop stopped selling drinks rich in E numbers, such as Coca Cola and Dr Pepper, and staff are convinced they have seen a difference in pupils.
"We now sell healthier soft drinks, including flavoured water, and the kids seem to love it."
Food expert Sarah Stanner, of the British Nutrition Foundation, said there was strong evidence that some children reacted badly to the additives in fizzy drinks.
But she said the number of children affected was small and she doubted that banning such drinks would make a major difference to a school's behaviour problems.