Parents who take their children to have separate measles, mumps and rubella vaccinations instead of the combined MMR may be at putting them at risk of the diseases and of unwanted side effects, according to a hard-hitting paper in a medical journal designed to stop the downward spiral in vaccination numbers.

The paper, in Archives of Disease in Childhood, and an even tougher editorial by a senior member of the public health laboratory service (PHLS), attack the controversial research of Andrew Wakefield and colleagues at the royal free hospital in north London which has suggested a link between measles vaccination and autism. Public health doctors are concerned that the boycott by many parents of the MMR will lead to a measles epidemic, which could claim children's lives.

Both papers attack Dr Wakefield's remark in 1998, which was not supported by his colleagues, that he considered the combined vaccination could overload the immune system. "He is yet to produce any sound scientific evidence to support this view," says the paper by David Elliman of the department of child health at St George's hospital and Helen Bedford of the institute of child health, both in London.

Yet many parents, worried by the suggestion of a possible link to bowel disease and autism, have leaped at the idea in hope of safeguarding their child. The Department of Health has refused to make individual vaccines available on the NHS, but some parents have travelled abroad to get them. The temperature of the controversy rose considerably recently when one GP, Peter Mansfield, was reported to the General Medical Council by Worcestershire health authority for giving individual vaccinations to those children whose parents asked for them.

Dr Mansfield was due to face a hearing this month to decide whether he should be suspended as an immediate threat to the public, but that has now been dropped and he continues to practise, although the GMC is still investigating the case.

The paper by Dr Elliman and Dr Bedford published today reviews all the evidence against the autism theory, says there is no basis for it, and finds that "there is no case for the use of single vaccines". They say there is "a large body of evidence to show that MMR vaccine is highly effective and only rarely causes serious side effects". The MMR has been used in the US for nearly 30 years, in Scandinavia for nearly 20 years and in the UK since 1988, they point out.

"In contrast, a regimen of giving single measles, mumps and rubella vaccine separately to pre-school children has never been used anywhere in the world," they write.

They warn that giving the vaccines separately at intervals means children are not protected against all three diseases as early as possible. "They are therefore at risk of catching one of the diseases while they wait to complete the course. This will allow continued circulation of the infections." Children would have to have six injections instead of two, and it was possible some would not return for all of them.

Single vaccines are not licensed in the UK, they say, and so "there is less control over what children are getting".

In a commentary, Elizabeth Miller of the PHLS admits that the BSE/CJD scandal has "fuelled concerns of some parents that the government experts might have got it horribly wrong, or worse still that there has been a cover-up".

But unlike BSE/CJD, the scientific evidence on the safety of the MMR is mountainous, she says. Dr Wakefield and colleagues' recent paper arguing that the literature had missed an important side effect - bowel disease - was "astonishingly naive", she writes. It was based on flawed statistics and omitted a large, important trial "that unequivocally refutes their claims".