Professor Peter Rubin said a draft BMA response to the GMC consultation on revalidation argued that the process should begin in areas 'where we think we are going to identify more problems'.
But the GMC view was different, he said. 'We have been of the feeling that we start where the systems are (already) in place, and that we move forward incrementally from there over the next three to four years.'
Professor Rubin said the GMC had met the BMA to discuss its response. He said there was much that the organisations agreed on.
The GMC chairman added that he had told the BMA that the regulator would 'carefully reflect' on its point of view.
He added: 'I don't know what the final response from the BMA will be, but there is much with which we agreed and I think there are all the makings of a constructive dialogue.'
A spokeswoman for the BMA said this was just one of the options the BMA was looking at, and emphasised that the response was a draft.
'The response is being redrafted at the moment and going out to comment,' she said, adding that it would be complete by the end of this week.
Professor Rubin also said the GMC 'had every reason' to think the new government will be supportive of revalidation. 'It will see appraisal as an integral part of the quality agenda, and it is a major part of revalidation. We have no reason to think anything other than (revalidation is) proceeding as planned,' he said.