The Chief Medical Officer called today for a central NHS register of expert witnesses to try to ease fears over miscarriages of justice.
Sir Liam Donaldson said changes were needed to restore confidence in the system both among the general public and within the medical profession.
Speaking as he prepared to publish a major review of how expert witnesses are used in court following a series of high-profile controversies, Sir Liam said: "It will be a very different system.
"At the moment it's a series of multiple small private agreements between individual solicitors and individual doctors.
"In the future the system will be brokered through the NHS. It will be teams of doctors, and in that way we will be able to ensure first that there are a wider number of doctors available to do this work, and also that their work is quality-assured and genuinely seen as a public good."
Sir Liam's study was commissioned in 2004, following a number of cases in which evidence by experts such as Professor Sir Roy Meadow led to convictions which were later ruled unsafe.
Angela Cannings walked free from a life sentence in 2003 after appeal judges cleared her of murdering her two baby sons. Prof Meadow gave evidence at her trial.
Days later, the then Solicitor General Harriet Harman announced that thousands of care orders in which expert evidence was decisive were to be reviewed under an inquiry which was also examining the convictions of 258 women for murdering their babies over the last decade.
Sally Clark was convicted in 1999 of killing her two sons after Prof Meadow told the court there was a "one in 73 million" chance that two children in the same family would die of cot death, but was also cleared on appeal in 2003.
Other women were also cleared of murdering their children on appeal or found not guilty at trials in which he gave evidence.
Prof Meadow - whose observation that "one sudden infant death is a tragedy, two is suspicious and three is murder, unless proven otherwise" became known as "Meadow's Law" - was struck off the medical register last year after the General Medical Council ruled he had "abused his position as a doctor" in giving the evidence he did.
The doctor won a High Court appeal against the GMC ruling earlier this year, but the medical body subsequently won its appeal against blanket immunity for expert witnesses.
Sir Liam insisted today that the number of cases where there were problems with medical evidence were very small, but change was needed - partly because young doctors were now too intimidated to take on the essential work.
He told the BBC Radio 4 Today programme: "It's something that younger doctors don't want to go into for a whole variety of reasons, including the very intimidating atmosphere that they perceive now surrounds this.
"So we need to get the quality right, but we also need to make sure there are enough doctors prepared to take on this sort of work in the future.
"What we want to see is competent medical experts and that's what we're aiming to do with this report. I'm not criticising the existing experts. The problem is there is a relatively small number of people doing it and all the work falls into a small number of hands, and therefore it also leads to inefficiencies in the courts system."
Lib Dem MP Dr Evan Harris (Oxford West and Abingdon), a member of the Commons Science and Technology Select Committee, said it was "critical" that medical expert witnesses were treated fairly.
"The public attacks - and indeed witch hunts - against doctors working in this difficult area, who are not allowed to defend themselves in the media, only serves to deter medical professionals from working in the area of child protection," he said.
"The price of avoiding future cases like Victoria Climbie, where a succession of doctors failed to consider abuse or report their concerns leading to a tragic death, is occasional investigations and even prosecutions of innocent parents.
"We rely on the courts to prevent miscarriage of justice in these cases as in all other areas."