The warnings system was introduced five years ago, but GMC chief executive Niall Dickson said it had not been absolutely clear what would happen to the warnings after a five-year period had ended.
'We said the warning would be "up" after five years, but what does that mean?' he said.
Mr Dickson said the GMC sought legal advice, and was told this was a matter of balancing the public right to access against the doctor's right to privacy and fairness.
The advice also outlined that doctors who have had a warning had an expectation that it would only last for five years and after that it would disappear from the front of the register, Mr Dickson said.
'We thought about that and decided that that was the right thing, not only for the doctors who have had warnings up to now, but all future doctors,' he said.
'So when you get a warning it will be on your record for five years. The warning is basically saying we are not saying your fitness to practise is impaired, but we are saying that we have concerns and that you need to do something about them.'
But Mr Dickson added that while the warning will be removed from the public domain, it will still remain part of a doctor's fitness-to-practise history.
'If an employer were to ask: "Is there is anything more about this doctor's fitness-to-practice history?" then we have an obligation to tell that employer about the previous fitness-to-practise history, including warnings that are spent,' he said.
'But that would not be in the public domain. And I think this is a proportionate and fair way of handling this issue.'
The GMC is set to make amendments to secondary legislation, which limits retention of the warnings to five years.