Advisers from both the DoH and the GMC revealed the level of uncertainty that remains about the system at the NHS Employers' conference in Birmingham last week.
Dr Nick Clarke, DoH head of health and social care regulation said that ministers were waiting for evidence from revalidation pilots that the system 'works and is affordable for the Treasury and doctors'.
He added: 'There are many, many costings that will have to be done. We need to learn from the pilots that this is affordable and not overly bureaucratic.'
Paul Buckley, GMC director of education and revalidation said: 'We are very conscious in light of tighter finances of doing this in a way without unnecessary burden on the NHS and the profession.'
RCGP Scotland chairman Dr Ken Lawton told GP that the financial crisis 'could not have come at a worse time for revalidation'. 'We're in fiscally constrained times, and revalidation has come along. There is still a lot of debate about how much it will cost and who will pay.'
He said the future of revalidation was 'a dynamic situation, especially with the political uncertainty down south'.
Dr Lawton said the RCGP shared anxiety about the costs of revalidation, but warned that a 'watered down' system may not be fit for purpose.
'We have to look at the tools we already have and how to give people access with minimal cost,' he said.
BMA chairman Dr Hamish Meldrum said a watered down revalidation system was preferable to an 'all-singing, all-dancing', but underfunded one.
He added: 'There is serious concern that some of the proposals are far too elaborate given the level of funding available.' He said the cost of multi-source feedback, and administering data from appraisal and clinical governance may be too high.
Meanwhile, GMC chairman Professor Peter Rubin told the RCGP conference in Glasgow last week that revalidation costs would vary hugely because some areas had invested in professional development while others had cut funding.
In a debate on revalidation, he slammed 'deluded' primary care organisations (PCOs) that fail to support GP appraisals.
Professor Rubin said: 'Appraisal is a non-negotiable part of professional practice.
'Any chief executive of a PCO who thinks they can run a class act without appraisal of their most important staff, I think is deluded.'
RCGP chairman Professor Steve Field said some PCOs had stopped appraising GPs to save money. He said: 'Those chief executives have no clue about professional development.'
He said he had also received complaints from appraisers that PCOs were not supporting them in difficult cases where GPs had refused to collect evidence for revalidation.
RCGP revalidation lead Professor Mike Pringle said new guidance, called Strengthening Medical Appraisal, would set down standards to be followed by every NHS organisation.