Health Secretary John Reid has called for an inquiry into claims that controversial research linking the MMR vaccine to autism was "flawed".
Children are vaccinated against measles, mumps and rubella
He urged the General Medical Council to investigate "as a matter of urgency", after the Lancet medical journal said it should not have published the study.
Richard Horton, editor of the Lancet, told the BBC the researchers had a "fatal conflict of interest".
Chief researcher Dr Andrew Wakefield rejected the journal's claims.
But the Department of Health said it welcomed the Lancet's regret for publishing material that had caused so much public concern.
Earlier Liberal Democrat MP Dr Evan Harris - a former hospital doctor - said parents worried about MMR needed a fully independent inquiry into the study in the Lancet and related research.
The paper, published six years ago, prompted many parents to reject the three-in-one jab, even though most experts say it is safe.
The Lancet launched an investigation into the way the study was carried out after it received an "allegation of research misconduct" from the Sunday Times.
The allegations do not cover the actual findings of the study.
On Saturday Dr Horton told BBC Radio 4's Today programme that Dr Wakefield had been commissioned by the Legal Aid Board to do a separate study to what was reported in the Lancet.
Some children were involved in both trials, which took place at London's Royal Free Hospital, he said.
Dr Horton said the goal of the Legal Aid Board-funded study was to find out if there was evidence to support a multi-party litigation case by parents who claimed the MMR jab had harmed their children.
"We did not know that he had a dual role with the Legal Aid Board in that he was doing this study separately from his Lancet investigation...and we certainly had no idea that he had received money to do that."
Dr Horton said Dr Wakefield had accepted the facts of his dual role and that he had received money from the Legal Aid Board, but denied a conflict of interest.
"That seems to me perverse," he said.
"He clearly had a conflict of interest which was very much against our rules in 1998 about declaring such conflicts."
Earlier, Dr Horton said: "If we had known the conflict of interest Dr Wakefield had in this work I think that would have strongly affected the peer reviewers about the credibility of this work and, in my judgement, it would have been rejected."
He told Today he believed the MMR jab was "absolutely safe".
Dr Wakefield said the Lancet study and his other work were completely separate and that he had not been involved in the selection process for the second study.
He said he believed his findings were still valid.
"They have now been confirmed independently by reputable physicians and pathologists."
He added: "My colleagues and I have acted at all times in the best medical interests of these children and will continue to do so."