Professor John Britton, a respiratory physician from Nottingham City Hospital, said that antioxidants in fruit and vegetables are vital to healthy lungs.
In addition, they would help improve children's general health.
Professor Britton was speaking at the British Thoracic Society's summer meeting for lung specialists in Harrogate, North Yorkshire.
He cited one study of more than 4,000 Italian children which showed that those who ate large amounts of citrus and kiwi fruits experienced less wheezing and asthma than others who did not.
And earlier this year a team from St George's Hospital Medical School, London, found that good lung function was associated with high intakes of vitamins C, E, and beta-carotene, citrus fruits, apples, and fruit juices.
Professor Britton said: "People with high levels of antioxidants in their diet should be more able to deal effectively with inflammatory lung disease.
"More and more evidence is accumulating that a balanced diet - including fruit and vegetables - can help children and adults to breathe more easily.
"The government must consider targeted ways of improving child nutrition.
"Free fruit in schools is just one direct and effective way of improving the lungs and hearts of the nation's children."
The professor also had a number of other suggestions for the Government.
They included levying a "junk food" tax on fizzy drinks and crisps, stricter nutritional standards for school meals, and a "supermarket summit" to review the price of fruit and vegetables in UK supermarkets.
Public health minister Yvette Cooper said: "A recent government survey showed that most children and young people do not eat enough fruit and vegetables.
"We are currently considering a range of options to improve the access to healthy food, particularly in those areas where it is expensive or hard to find."
Rates of childhood asthma have increased markedly in recent years. The cause is unknown, but some believe it is linked to an increase in air pollution, or to greater exposure to house dust mites, which thrive in modern living conditions.
It is thought that high levels of antioxidants may be important in protecting the lungs from the harmful effects of atmospheric pollutants and cigarette smoke.