The shortage of primary school deputy heads is even more serious than the gathering headship crisis, according to the latest figures from the Department for Education and Employment - suggesting further, long-term recruitment problems for the Government.

Vacancies for deputy heads are running at more than one-and-a-half times the rate for heads, a worse position than in 1990, which saw the teacher shortages reach their peak. There are now proportionately more empty jobs for deputies than for any other type of post.

Moreover, the figures are taken from January - before the Conservative Government triggered a rush of resignations with its plans to end early retirement.

Headteachers’ leaders blamed the lack of rewards for deputies, along with the increasing pressures of the job. According to the National Association of Headteachers, the crisis threatens to scupper government plans for a national headship qualification - which is aimed at aspiring deputies.

Meanwhile, new figures from Cambridge University show that the shortage of secondary school science teachers is growing. The lack of PGCE students in the field appears to have fed through to actual teacher vacancies, which are worse this year than last.

The lack of headteachers has already been identified as one of the most serious problems facing primary schools - a sector which has been picked out for special attention by the Government and is the main target for its literacy and numeracy campaigns.

The last government’s threat to scrap the early retirement scheme appears to have made the problem worse, with the vacancy rate shooting up since the start of the year.

Advertisements in The TES for the first four months of the year show primary headship vacancies at 40 per cent above last year and nearly 60 per cent higher in the secondary sector.

According to the latest figures from the DFEE, there are 131 vacant primary headships in England and Wales, 0.8 per cent of the total teaching population. But there are 218 vacant deputies posts (1.3 per cent of all teachers).

The overall picture is not yet as grave as it was in 1990, when 352 schools were without a head, and 402 without a deputy. But recruitment analysts believe such a position is not far off, and that the lack of deputies threatens to be much worse than 1990.

“The incentives to become a head have diminished over the years, not least in salary terms,” said the general secretary of the NAHT, David Hart. “I’m not in the least surprised that there should be a growing crisis in the filling of deputy posts. The shortage of heads and deputies will be an enormous headache for the government. It places a question mark against the new professional qualification.”

Without deputies, he said, there would be no recruits for headship.

Last month, Education and Employment Secretary David Blunkett announced that a National Professional Qualification for Headship will eventually become compulsory for would-be heads.

Mr Hart said the differences in pay between deputies and other senior teachers should be increased, and called on Education and Employment Secretary David Blunkett to raise the shortage with the School Teachers’ Review Body.

The lack of science teachers is also causing concern. A new analysis of job advertisements in The TES show that science vacancies have been more numerous in 17 out of the 21 weeks up until May than in the same period last year.

Felicity Eaton, a research associate from the University of Cambridge School of Education, and fellow researcher Gabriel Bennet say they have found “a sharp increase in the number of vacancies advertised in The TES, most weeks showing significantly more vacancies than this time last year”.

Posts of added responsibility - such as heads of department - are particularly hard to fill.