By Adam Brimelow
BBC radio health correspondent
The GMC is to seek leave to appeal against a High Court ruling giving expert witnesses immunity against disciplinary action.
Sir Roy denied serious professional misconduct
The ruling was made in the case of paediatrician Professor Sir Roy Meadow, who had given evidence on cot death risk in the Sally Clark murder case.
The General Medical Council believes the ruling sets down a new principle of law, the BBC has learned.
The GMC says it could affect the work of all regulatory bodies.
Professor Sir Roy Meadow appeared before the GMC after giving what was later found to be flawed statistical evidence he gave in the trial of Sally Clark, who was wrongfully convicted of killing her two baby boys.
He had said the chance of two natural cot deaths in her family was one in 73 million.
The figure was later disputed by the Royal Statistical Society and other experts said that once genetic and environmental factors were taken into consideration, the odds were closer to 200 to one.
Sir Roy also gave evidence as an expert witness in the trials of two other women, Angela Cannings and Donna Anthony, who were both freed on appeal after being convicted of murdering their children.
A GMC fitness to practise panel found him guilty of serious professional misconduct and ordered that the retired paediatrician be struck off the medical register.
But that decision was overruled last month by a High Court judge.
Mr Justice Collins said Sir Roy had "made one mistake, which was to misunderstand and misinterpret the statistics". He said it was a mistake that was "easily and widely made".
Sally Clark: Served three years after being wrongly convicted of killing her two sons
Angela Cannings: Served 18 months after being wrongly convicted of killing her two sons
Donna Anthony: Served six years after being wrongly convicted of killing her son and daughter
Trupti Patel: Acquitted of killing three of her children
He also concluded that expert witnesses should be immune from disciplinary proceedings unless referred on by the trial judge.
The GMC's findings against Sir Roy had "increased the reluctance of medical practitioners to involve themselves in court proceedings", he said. The medical regulator has now said it will lodge an application for permission to appeal against Mr Justice Collins' judgement on Thursday.
The GMC's chief executive, Finlay Scott, told the BBC that it would not try to restore the original decision that Sir Roy Meadow's name be erased from the medical register.
He added: "The appeal will primarily be about very important points of law.
"In particular we want to challenge Mr Justice Collins' introduction of a wholly new principle of law, which is that doctors and other professionals who give evidence enjoy immunity from disciplinary proceedings."
He said the GMC wanted the Appeal Court to issue guidance on when the regulator should get involved in such cases and that this should be when there was criticism by the judge, or other "substantive evidence" that a doctor has fallen below accepted standards.