The medical journal The Lancet has said it should never have published the paper by Dr Andrew Wakefield because of the way in which his research had been funded.
It says it represented a "fatal conflict of interest." This afternoon, the Health Secretary Dr John Reid backed a call for an independent inquiry, and urged the General Medical Council to begin an investigation "as a matter of urgency."
Our Social Affairs Correspondent Victoria Macdonald explains.
This is the 1998 paper published in the Lancet which is now at the centre of fresh controversy surrounding Dr Andrew Wakefield and the possible link between MMR, bowel disease and autism.
It is now alleged that Dr Wakefield had failed to mention that he was working on a study to see if there was evidence to support a legal action by parents claiming the MMR jab had harmed their children.
The Lancet says there was a clear conflict of interest. That if they had known about the legal aid they would have removed the section on MMR.
One MP has called for a public inquiry although the Health Secretary said today it should be referred to the General Medical Council.
In a newspaper tomorrow, a number of other allegations will be made against Dr Wakefield. Among them, that ethical approval was not given for the investigations on the children.
This is denied by Dr Wakefield, his colleagues who contributed to the paper, and the Royal Free Hospital in north London where he worked at the time.
It is also alleged that some of the £55,000 legal aid money was for work that had already been paid for by the NHS. Again he denies this. He said some money was paid towards a research assistant.
The controversy over MMR has led to a dramatic downturn in vaccination rates which is only now righting itself.
Before the research, in 1995-96, 92 per cent of children under two in England were immunised against MMR. By 2002 this had fallen to 84 per cent.
And by March last year it had fallen under 82 per cent.
Yet is hard to remember in all this that the original Lancet paper contained just one paragraph stating that the parents had raised concerns about a link between the vaccine and autism.
The main thrust of the paper was identifying a possible new bowel disease in autistic children - vital research which even the Lancet today says was entirely valid.
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