GMC president Professor Sir Graeme Catto said: 'It is a new law and should any doctor feel it wasn't applied fairly, I suspect, as with any major change, we will end up in the High Court.'
The introduction of the civil standard of proof in fitness-to-practise cases, rather than the criminal standard, will start from April 2008, the GMC hopes.
The GMC has published a summary of responses to the consultation on how the changes should be implemented.
Almost without exception, responses from individual members of the profession argued against the civil standard of proof, the report said.
The GMC president was defiant, saying: 'We are talking about 50 doctors out of all the doctors in the country.'
The consultation was meant to establish how to implement the changes, but the BMA was frustrated that there was no consultation on whether to make the changes in the first place.
Paul Phillip, GMC director of standards and fitness to practise, said there were many organisations in favour of the move and that most government regulators used the civil standard. He later admitted that the majority of health organisations were probably against the move.
GPC chairman Dr Richard Vautrey said the BMA would continue to fight to reverse the decision. 'Doctors remain to be convinced. Under huge pressure, in high-profile cases, you can see the GMC making decisions that might not be fair.'
Sir Graeme said: 'It would be helpful if the BMA had seen the advantage of the move. It allows us to address the less serious cases we see to ensure doctors abide by conditions of practice.'
Under the new standard, a fact will be established if it is more than likely to have happened. The current criminal standard means a case must be proved beyond reasonable doubt.
The GMC has said the civil standard will be flexible, meaning serious allegations will require more convincing evidence.