HSJ has learned that NHS London does not have sufficient money in its budget to cover the£3m it has spent matching junior doctors to training posts.
The SHA has asked the Department of Health to fill the funding gap, but fears the money may come out of training programmes.
Minutes from a board meeting have revealed that the local deanery, tasked with managing the recruitment process after the failure of the Medical Training Application Service, has not had the capacity to cope alone.
External consultants and up to 40 temporary staff a day have been working to sift through the 23,000 applications for just under 4,500 jobs.
Nearly every trust in the capital has contributed to the effort by donating up to three human resources employees.
NHS London director of people and organisational development Anne Rainsberry said: 'The deaneries quickly had to switch to a paper-based system, looking at applications of at least 10 pages long.
'The pressures that were created were bound to cause difficulties. We've risen to the challenge by not missing deadlines and getting an 87 per cent fill rate.'
London has the biggest workload of all SHAs, but other regions have also felt the pressure, she said.
Matt Jameson Evans from junior doctors' campaign group Remedy UK agreed the problem was not confined to London. 'Staffing in the deaneries is in a crisis. It's difficult to get hold of them as they don't have the capacity,' he said.
NHS South Central has brought in extra administrative support to cope and NHS South East Coast said it was 'working closely with trusts'.