Professor Peter Bramley at the University of London, working with colleagues in Japan and Germany, has developed the tomatoes which are rich in beta-carotene.
Beta-carotene is turned by the body into vitamin A, which is thought to be crucial in preventing serious disease.
The United Nations Children's Fund (UNICEF) estimates that each year between 1m and 2m deaths of children aged between one and four could be prevented if they received more Vitamin A.
The researchers said that increasing the amount of beta-carotene, and other carotenoids, in foods was generally though to be more effective than taking supplements in the form of pills, as other nutrients in the food act alongside the carotenoids.
Professor Bramley said processed and tinned tomatoes had been found to be more healthy because they improve the take up of carotenoids.
They said in the journal Nature Biotechnology that the genetic changes would last for at least four generations, making the vitamin-packed fruit available long-term.
As well as fighting off cancer and heart disease, vitamin A has also been linked to preventing macular degeneration, and eye condition that can lead to blindness.
They altered the carotenoid biosynthesis pathway by inserting a gene from a bacterium. The gene converts the compound phytoene into lycopene, which in turn is involved in the production of alpha and beta-carotene.
Three times normal levels
The resulting tomatoes contained up to 3.5 times the normal levels of beta-carotene, although overall levels of carotenoids - of which there are several, including lycopene - did not change.
The researchers said they had expected the gene to also cause the tomatoes to produce extra lycopene, but it did not.
Lycopene is also important to health and tomatoes are the main source of that nutrient in most people's diets.
Dr Sue Meyer, of Genewatch, was not convinced by the benefits of the genetically modified fruit.
She told BBC Radio 4's Today programme: "If we can prove it was safe and a genuine improvement, it would be welcome.
"But if you change the basic biochemistry, you could alter the levels of other nutrients which are very important for health."
Professor Bramley told the BBC that trials were now underway to ensure the tomatoes were safe for human consumption.
He added: "Nobody is suggesting right now that we are going to feed this to the population."