Offering single vaccines for measles, mumps and rubella would be playing "Russian roulette" with children's lives and lead to a resurgence of the potentially fatal diseases, the Government's chief medical officer warned yesterday.

Professor Sir Liam Donaldson made clear he would resign if ministers "capitulated" to pressure to abandon their current policy of only providing the combined MMR vaccine on the NHS. He ruled out calls for parents to be given the choice of individual jabs, saying they would have no scientific justification, and suggesting immunisation rates would fall as a result.

Idis World Medicines, a supplier of the unlicensed single vaccines, said it was running short of stock, such was the demand from parents worried about the alleged link between MMR and autism. Sir Liam said: "We would have to accept the certainty of more cases of these diseases because uptake rates would fall and we would be doing so in the face of major evidence in favour of MMR. We would be out on a limb compared with 90 other countries.

"We would be playing Russian roulette with our children's health and that, in my view, would be an irresponsible and ineffective way to run a programme which is meant to protect children's health."

Sir Liam indicated he would resign if the Government gave ground."I would be in a very difficult position and so would all my colleagues in the Department of Health," he said.

There would also be a vociferous backlash from the medical colleges and other scientific bodies, he said, because there was no scientific proof that the MMR jab was linked to autism in children.

More and more parents are refusing the MMR jab for their children because of fears, triggered by the scientist Dr Andrew Wakefield, that the vaccine could be linked to autism and bowel disorders. The controversy has been heightened by four outbreaks of measles in which school-age children and infants too young to be immunised have been infected by the virus.

Dr Wakefield, who now works in the United States, returned to the fray yesterday when he said it was "unsustainable and reprehensible" of the Department of Health not to offer parents a choice.

But ministers hoped that Sir Liam's strong statement would head off a crisis of public confidence over the MMR vaccine.

"The message is getting through; there is no plan B," one source said.

Sir Liam said a single vaccine programme simply "would not work" and would have a "disastrous" effect. Children would be unprotected for longer periods, he said. They would require six jabs instead of two and this requirement on parents would lead to a steep decline in vaccination rates. Professor Donaldson recalled the 1970s when a similar controversy raged about a combined whooping cough vaccine.

Ministers gave in to demands for separate jabs. The uptake rate fell to 30 per cent and took 15 years to recover. A quarter of a million children got whooping cough and 1,000 children a year were in hospital with severe meningitis.

"We have been there before," Sir Liam said. "To capitulate to media pressure in light of strong scientific evidence ultimately damages children."

Referring to Dr Wakefield's latest suggestion that the measles virus was an "immunological trigger" for bowel disorders, Sir Liam said the research appeared highly flawed. It was being studied by scientists who had already "picked up a number of serious inconsistencies and problems in the methodology".

He said autism had a strong genetic basis. If it was linked to MMR, it was strange that 70 per cent of cases of autism were in boys, even though equal numbers of boys and girls were vaccinated.

In California, cases of autism increased in the late 1980s and early 1990s, some 15 years after MMR was introduced. In Britain there was a fourfold increase in autism in young boys between 1988 and 1993 when MMR rates were constant. In Finland, a study of 1.8 million children who had MMR found no link with bowel disease or autism, he said.

Private doctors, who are charging up to £300 to give children three individual jabs, also reported a tenfold increase in inquiries from parents this week. Dr Peter Copp, medical director of the GP-Plus private clinic in Edinburgh, said: "We have been overwhelmed with inquiries. We may set up a temporary clinic in Glasgow."

The clinic, which charges £280, has immunised 3,500 to 4,000 children in 18 months. Dr Copp said about £70 covered the cost of the imported vaccines. A Department of Health spokesman said that in the developing world, single vaccines cost about 10 cents each.