The Attorney General has told appeal judges it is not up to a court to decide if expert witnesses should be immune from disciplinary action.
Sir Roy was initially struck off the medical register
Lord Goldsmith intervened to back an appeal by the General Medical Council over the case of paediatrician Professor Sir Roy Meadow.
Sir Roy was struck off for giving flawed evidence at Sally Clark's 1999 trial for the murder of her sons.
However, the High Court over-turned the decision in February.
It ruled that regulatory bodies such as the GMC could not punish expert witnesses over "honest mistakes" - and that to do so would deter others from giving evidence.
Under the ruling, cases could only be referred to disciplinary bodies by the trial judge.
The GMC believes this decision undermines its role, and that of other professional regulators, and is asking for it to be overturned by the Appeal Court.
The hearing will not focus on Sir Roy's case, but on the GMC's ability to consider similar cases in future.
The GMC says it agrees doctors should not be deterred from giving evidence, honestly and truthfully, and within their competence.
But it has concerns over the proposal to give the trial judge the remit to decide if a professional body should investigate an expert.
It also suggests the ruling contradicts its duty to investigate any complaint which could be found to amount to serious professional misconduct.
Lord Goldsmith told a panel of three judges sitting in London he was not seeking to raise any issues about Sir Roy's conduct, or the GMC's decision to strike him off.
However, he said immunity for expert witnesses should not be an issue for the court to have to decide.
He said: "It is crucially important that expert witnesses should assist the court conscientiously and objectively, rather than being tempted to give any evidence that suits their client's case.
"To that end, the threat of fitness to practice proceedings against them provides an important check which is calculated to assist significantly in the administration of justice and also to promote public confidence in the judicial process."
John Batt, a lawyer who advised Mrs Clark's legal team, said he was also concerned about the ruling.
He told BBC Radio 4's Today programme: "The effect of this new law by Mr Justice Collins is it, in effect, neuters any professional bodies... who have experts who give evidence in court.
"It means they can't take any action against them no matter how badly they behave."
But Tom Magner, from the Society of Expert Witnesses, said it was "essential" for experts to be protected by the courts from disciplinary action by professional bodies.
He said: "If expert witnesses are deterred... it restricts the pool of expertise that's available to the courts and must therefore effect the ability of the court to make fair decisions."
Professor Meadow gave evidence at the trial of Sally Clark, who was arrested in 1998 after the deaths of her two sons, Christopher and Harry.
He told a Chester Crown Court jury there was a "one in 73 million" chance of two children dying from cot deaths in an affluent family.
Mrs Clark's conviction was later quashed in the Court of Appeal on grounds unrelated to Professor Meadow's evidence.
Mr Justice Collins, the High Court judge, ruled that, not only was the GMC unjustified in making a finding of serious professional misconduct last summer, it had no right to pursue the complaint in the first place.
He said expert witnesses must be immune from any disciplinary action - save in exceptional circumstances - so that they are not deterred from coming forward.
This was both because they should not be disciplined for an "honest mistake", but also on the grounds that since a witness enjoys immunity when giving evidence in court, that evidence could not form the basis of a disciplinary charge.
He said it was "quite unnecessary" to erase from the medical register someone like Professor Meadow who he described as a first-class paediatrician to whom many families owed much over his dealing with their children.