Hundreds of vacancies remained unfilled after the first recruitment round.
For the first time ever, the National Recruitment Office for GP Training did not have enough eligible applicants and was forced to run a second recruitment round to fill almost 300 vacancies.
Some training posts will remain unfilled this year after the recruitment office failed to find suitable applicants in the second round.
The plummeting numbers applying for general practice come as GP training programmes are poised for a huge expansion.
GP registrar vacancies in England are set to rise from 2,700 in 2009 to 3,300 in 2011.
The sharp drop in applications will fuel moves to stop year-on-year reductions in the registrar's supplement.
The Doctors' and Dentists' Review Board recommended a drop in the supplement to 45% this year after recruitment remained strong in 2008.
But registrars claim that the drop from 65% has driven recruitment down.
Dr James Parsons, a GP registrar in Sheffield and a member of the GPC trainees subcommittee, says that registrars' pay is ‘below the average that junior hospital doctors get'.
‘People are really hacked off with the cut in pay year on year. It is an immediate deterrent.'
The BMA is surveying GP registrars on their hours and work intensity.
An NHS Employers spokesman said: ‘We do not believe that take-up of GP training places is directly related to the supplement change.'
It wants the registrar supplement better aligned with hospital supplements. Once hospital doctors comply with the European working time directive, their supplements will range from 0-50% of salary.
- Read this week's GP dated 10 July for the full version of this story
- Editor's blog: Why partnerships should be incentivised
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