The influential independent schools' organisation barred Winchester's new acting head Tommy Cookson from joining this month because of "issues of governance and management" at the pound;16,000-a-year private school.
Mr Cookson, a former Winchester housemaster and retired Sevenoaks school head, said he was disappointed by the HMC's decision. "No school would be happy with this," he said.
The suspension appears to be linked to resistance by governors to reforms to the school instigated by Winchester's previous head Nick Tate, the former head of the Qualifications and Curriculum Authority. He resigned in February.
Mr Cookson confirmed there had been disagreements. "There are always difficulties when a school moves from one point to another, and there will always be some people who agree with it and some people who don't," he said.
But he insisted that Dr Tate's decision to leave the school was entirely based on family reasons which had previously been reported. Dr Tate's son Oliver, a former Winchester pupil, had been reprimanded for smoking cannabis and had set light to a car belonging to television journalist Martin Bashir.
Mr Cookson said he planned to continue the reforms started by Dr Tate, which included a review of the school's senior management, and was confident it would be readmitted to the HMC.
The only two other schools to be suspended by the HMC in the past decade are Cheltenham college and Bristol Cathedral school, which were both temporarily excluded after clashes between governors and heads.