They also called for the DoH to produce accurate five- to 10-year forecasts of workforce requirements so that both graduates and training organisations 'know where they stand'.
The move follows the decision by the London Deanery earlier this year to defer GP specialist training courses for 29 doctors for six months (GP, 30 June).
Dr Dick Savage, a London course organiser, said all junior doctors' training was under threat because of a 'dangerous cocktail' of short-term thinking and desperation to cut costs.
'We need to know funding is in place for at least the duration of the training programmes - for general practice that means three years,' he said. 'A deanery cannot function when the education budget is not fixed by the DoH until six months of the financial year have elapsed.'
The organisers also called for the London SHA to step in to reverse the deferment of GP training courses.
Meanwhile, the GPC said that the 29 doctors affected by the London training cuts had been found alternative work until their training started. One, however, is understood to have moved to New Zealand to take up a short-term post.
GPC negotiator Dr Richard Vautrey said: 'Most of the jobs have relevance to general practice, and most are in a similar geographical area.'
A DoH spokeswoman said: 'It is the responsibility of PCTs and SHAs to analyse their local situation and develop plans, in liaison with their local NHS trusts and primary care providers, to deliver high-quality NHS services and take action to recruit the appropriate staff required to deliver these services.
'Training budgets are reviewed each year based on numbers of trainees expected to be in post,' she added. 'This ensures that adjustments can be made to reflect issues such as dropping out from training or recruitment problems.'
Last week the Conservative Party claimed that NHS workforce training budgets had been cut by £150 million in 2005/6 to offset deficits.
The DoH said: 'This is back-of-an-envelope speculation.