Dr Nick Tate said the Qualifications and Curriculum Authority would broker deals with exam boards to protect worthwhile, but uneconomic, qualifications in return for the rights to offer mass-appeal subjects such as maths or English.
But he said the QCA would allow genuinely redundant subjects to die, countering criticism that public money is wasted on subject areas no one wants.
Dr Tate spoke as it emerged that the exam board Edexcel had dropped A-levels in Arabic, Hebrew and Turkish, claiming they were too expensive to run.
He said that exam boards have a "public duty to offer qualifications where there's a very small take-up", adding that "we have been quite concerned over the past few years with the threat to certain subjects".
According to Edexcel, 120 students took Arabic A-level in 1996 while the same number were examined in Turkish. Up to 70 students took Biblical Hebrew and 50 took Modern Hebrew.
A board spokeswoman said: "Edexcel is a charity and can't afford the huge cost of running these courses when so few people are taking them."
Edexcel puts the cost of developing a language syllabus at Pounds 10,000 and the running cost of one of these courses at Pounds 30,000, and claims they are uneconomic.
Mona Mohamed, head of Manchester Islamic High School, said: "The Muslim community is very angry about this. We were planning to introduce Arabic A-level from this September and our Arabic teacher had spent the year preparing a syllabus. Now she will have no job and many students will be unable to study Arabic at university."
Nadia Abdelaal of Arabica, a group which promotes the teaching and learning of Arabic in Britain, has formed a committee which is fighting to save the A-level by persuading other boards to consider it.