The warning came after health minister Dr Dan Poulter wrote to the NHS Pay Review Body, which advises the DH on NHS staff pay, last week to set out its remit for 2014/15.
The letter echoed advice from chief secretary to the Treasury Danny Alexander that 'pay restraint remains a crucial part of the consolidation plans that will help to put the UK back onto the path of fiscal sustainability'.
It also quoted a letter from Mr Alexander stating that 'there are unlikely to be significant recruitment and retention issues for the majority of public sector workforces over the next year'.
But GPC negotiator Dr Dean Marshall said this was an 'interesting assessment of the current situation in the NHS'.
He warned: 'GP have had a year-on-year decrease in funding, in an environment where there has been a huge increase in demand and a huge transfer of work from secondary care, and the government appears to be trying to ignore it.
'On the ground there are huge problems with recruitment and retention, we can’t get locums, can’t get partners, can’t get people to take salaried roles.
'Every year we rely on doctors who have just qualified as locums but they are increasingly going abroad.'
Recruitment problems to other posts meant this pool of young GPs was 'spread thinner than before', he said.
Dr Marshall said the picture across the UK was varied, but that recruitment had been hit by rising workload and the move to 'less appealing' tick-box medicine.
A DH spokeswoman said the department would write to the DDRB soon.