Peter Peacock added that pupils believed the school system was "upside down" in giving them four years to prepare for Standard grade exams and only a year for the more important Highers.
Giving evidence on his reform programme to the parliamentary education committee, Mr Peacock said it was time to allow pupils to decide earlier which subjects they wanted to study in depth and not to stand in the way of those who wanted to sit Standard grades or equivalent National Qualifications in S3, freeing more time and space for Highers.
Outlining the Scottish Executive's thinking behind its plans for reforming the school curriculum, Mr Peacock said that pupils would still experience a broad range of subjects in S1, but would choose their main subjects at the start of S2. This would leave them space to concentrate on literacy and numeracy in depth and to experience new areas such as the arts, enterprise education and vocational courses.
Some pupils would then be able to take their Highers over two years - improving their chances of gaining better grades - or allow some to sit two batches of Highers over two years and gain other experiences at the same time.
Mr Peacock told the committee he thought the education system had erred in leaving the choice of further study until the end of S2. "It is increasingly evident that young people could make more choices at the end of S1," he said.
"I have seen schools already doing that - young people working on a much narrower set of subjects but looking in depth at literacy and numeracy and applying that space to music, drama, enterprise education, or vocational courses."
Mr Peacock added: "One of the very strong impressions I have had coming back into education in the past 18 months is how much we have, through the 5-14 guidelines and the focus around Standard grade, squeezed out of traditional school life a number of things that used to be valuable, like sport, music or drama.
"If a pupil is not choosing one of these things as a route of study, they would not form part of his or her school environment.
"We know that schools which have been bringing these things in earlier get better motivated kids all round. Their learning improves and their engagement with school improves."