London remains the worst-affected area: out of 110 headships advertised in the past year, 47 remain unfilled. Nationally, one-quarter of headship vacancies are unfilled.
Trainee recruitment is also down, with 5,000 fewer graduates applying for secondary teacher training courses than the Government had hoped for.
The figures, compiled for the National Association of Head Teachers, fly in the face of ministerial pledges to raise standards.
David Hart, the NAHT's general secretary, warned that the recruitment crisis placed "a time bomb" under the Government's education policies. He told his union's annual conference in Eastbourne: "Good honours graduates are voting with their feet and seeking other jobs where the salaries, benefits and overall conditions of employment are more attractive.
"The Government may well have inherited an appalling situation from the previous administration, but education is a top priority on which it intends to go to the electorate in 2002. It has only a very short period of time in which to take the urgent action necessary to make teaching an attractive proposition for the graduates of the future."
Maths, sciences, design and technology and modern foreign languages have suffered the biggest falls in applications compared with 1997.
Interest in primary teacher training is healthier, with applications almost 1,400 above target. However, the target does not take into account the Government's policy of reducing class sizes for five to seven year-olds.
John Howson, an independent education consultant and fellow of Oxford Brookes University, who compiled the figures, said: "If the Government continues to name and shame poorly performing schools, then those schools will be unable to attract teachers and the spiral of decline will continue.
"The situation in London has certainly reached crisis level. Teachers have a perception that it is not the easiest place to work in."
Mr Howson added that relatively poor pay and conditions were also dissuading many young people from considering teaching.
Separate figures released by the Department for Education and Employment last week show that class sizes have reached a record high under Labour.
NAHT conference, page 6