Art and design is the best taught subject, followed by history, music and English.
Maths teaching often fails to inspire, as many lessons are based on completing exercises from textbooks or worksheets without pupils being given the chance to build the deeper understanding needed for problem-solving, the chief inspector says.
Pupils in middle and lower sets appeared to be suffering disproportionately, as they were more likely to be taught by staff who had gaps in their knowledge.
Many pupils were also becoming disaffected because of "rigid setting arrangements" which gave them limited scope to do well.
Recruitment and retention difficulties were also significant for a rising number of schools, said the report.
The damning picture is painted in an eight-page paper supporting the report, which lists maths as one of the worst-taught subjects at key stage 4. Teaching was good or better in half of schools. However, at key stage 3, the national strategy had had a positive impact and maths teaching was good or better in 70 per cent of schools.
The teaching of citizenship is even weaker than maths, the report says. It was the worst taught at both key stages, with unsatisfactory provision in 26 per cent of schools.
Although it became a part of the national curriculum two years ago, some schools had introduced it very late. Unsatisfactory teaching was most often found where it was taught through other subjects.
In art and design, 29 per cent of lessons were judged very good or excellent.
The report said that overall, teaching quality was good or better in a majority of schools. But staffing problems were still affecting not just the teaching of maths, but science and religious education too.
Achievement was unsatisfactory in almost half of schools which were seriously affected by difficulties finding specialist teachers.