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Fears have been raised the vaccine against measles, mumps and rubella could trigger the developmental disability known as autism in some children.
But the Chief Medical Officer, Sir Liam Donaldson, insists there is no evidence to link the MMR with autism.
Vaccination rates have gone down by 5% in the past three years and there are fears a measles epidemic could follow.
Doubts were first raised about the safety of MMR in 1998 by Dr Andrew Wakefield, who works at the Royal Free Hospital.
He's calling for parents to be offered individual jabs: "For the moment there is doubt and where there is doubt further investigation is required and until that time that it is resolved scientifically, then the parents absolutely deserve the choice."
Autism was first diagnosed in the 1940s. It is a disorder which affects a child's ability to relate to other people and can lead to anti-social behaviour.
Dr Wakefield's theory is that the triple vaccine damages the gut, triggering inflammatory bowel disease which allows dangerous toxins to seep out into the bloodstream and up to the brain, triggering autism.
The biggest scientific study to date has been carried out in Finland where around two million children were tracked for 14 years. No link was found between MMR and autism.
Janice Ballard has an autistic son, Jamie. He had his MMR jab after being diagnosed as autistic.
Mrs Ballard says it is a difficult condition: "His behaviour can be quite distressing sometimes with head banging and hand biting.
"It takes a while to come to understand how he is and if he wants to do something, it's very difficult to channel him into other directions. He's absolutely obsessed with doing that thing."
Sir Liam says: "The vaccine has got a terrific record over the years. It's been in operation around the world for decades.
"Millions of children have been vaccinated and hundreds of thousands of lives have been saved.
"We've looked carefully at Wakefield's claims. He's a lone voice but nevertheless we haven't ignored him, but we can't substantiate his claims."
The MMR vaccine was introduced into Britain in 1988 - but until 1999 it was still possible to get single measles vaccines.
Single vaccines were also available for mumps and rubella but were not routinely given to all children.
Since August 1999, the government has banned importation of the single measles vaccines on the grounds that different types of vaccines may produce different levels of immunity and therefore leave children open to other strains of the disease.
Dr Wakefield's research in February 1998 was the first to suggest a link between the MMR, bowel disease and autism.
Since then, there have been numerous studies contradicting his findings - but fears persist and there have been mounting calls for the single vaccines to be made freely available.
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