Schools said that one in six teachers covering for the 3,000 vacancies in schools in England and Wales was poorly matched to the job, in a survey for the School Teachers' Review Body.
The problems were greatest in primary maths and information technology classes, subjects where schools are finding it hard to recruit, and in secondary humanities. More than a third were a poor match.
Heads in Merseyside said 70 per cent of covering teachers in all subjects were ill-suited to the job, three times that of any other region.
The findings are published in the Review Body's survey of teacher vacancies and recruitment, produced by the Office of Manpower Economics.
It found that headteachers turned to supply agencies to cover a quarter of all empty posts. A further third were filled by other supply teachers or teachers on temporary contracts of less than a term.
Jst over a quarter were covered by other staff within the school but 6 per cent were not covered at all, especially in primary schools.
The survey also found more continuing recruitment problems in inner London schools and in special schools, with vacancies running at more than 1.5 per cent - more than double the average for all schools.
Nationally, one in 20 posts went unfilled, but the figure rose to one in 12 in schools in inner and outer London, and to one in eight in special schools, which got an average of just five applicants per post.
Secondary maths and design and technology posts caused the most problems - technology teacher training courses under-recruited by 40 per cent last year, and the Government has just cut the target by a third.
David Hart, general secretary of the National Association of Head Teachers, said: "These findings simply reinforce the need of the STRB to ignore the blandishments of the Secretary of State who is trying to make them keep this year's pay award down to the bare minimum.