James Sabben-Clare, head of Winchester, said that his school, which regularly leads the A-level league table, might consider abandoning the exam and taking the International Baccalaureat instead.
Ministers have insisted that plans, to be announced shortly, to broaden the A-level will maintain its existing high standard. From September next year, pupils will be able to begin five subjects in the sixth form and take new AS exams at the end of their first year. They will then decide whether to continue with three A-levels, the usual number at present, or to carry on with more subjects.
The new courses will be offered in six "modules", or bite-sized chunks, with exams that can be taken throughout the two years and mixed with advanced vocational qualifications if pupils wish.
Both universities and state school heads have welcomed the changes, which were first proposed in a report by Sir Ron, now Lord, Dearing. Many independent school heads are also enthusiastic. Many maths and science A-levels are already modular and modular exams are growing in popularity in both state and independent schools.
But Mr Sabben-Clare, chairman of the Headmasters' and Headmistresses' Conference (HMC) of leading independent schools told officials from the Department for Education at a meeting last week that some academic schools were concerned about the preservation of traditional exams taken at the end of two years.
Exam boards will still be able to offer these exams but Mr Sabben-Clare said he feared that the decision to make modules the norm would affect the way all A-levels were assessed.
He said: "Modules seem to work quite well in subjects such as science, but at Winchester we believe that the changes will make subjects like history less seriously analytical. It will be reduced to a series of specified hoops and those with imagination will be penalised. Serious academic study of history will be compromised."
Winchester already offers international GCSEs for younger pupils. Mr Sabben-Clare said that if the fears about the new A-level were realised, he would consider opting out of the exam and putting pupils in for the International Baccalaureat, which requires a spread of arts and science subjects and a paper in the theory of knowledge.
Several leading independent schools, such as Malvern and Sevenoaks, already offer the IB.
Vivian Anthony, secretary of HMC, said: "There are some schools who feel that A-level as it is at present has served them well and whose particular concern is that it is not quite the challenge it was in the past.
"There are others who are clamouring for a broader range of subjects and more flexibility to do vocational qualifications alongside A-levels, which will be possible under the new system."
John Dunford, general secretary of the Secondary Heads Association, which represents state school secondary heads, said he had no worries about the standard of the new exams. "We are right behind these changes. It will lead to greater breadth and will enable students who at the moment drop out of A-level courses to get some accreditation for a worthwhile performance. I would not want to see any backtracking by the Government."