DH guidance requires that all GPSIs should have been reaccredited by primary care organisations by next month.
But GPSIs are warning that roll-out of the reaccreditation process has been patchy.
Confusion over how the process should work could lead to variation in standards and undermine the development of advanced GP roles that can drive integration between primary and secondary care, they warned.
Dr Martin Johnson, a pain management GPSI in South Yorkshire, said national guidance needed to set out what competencies people need and define a standard that GPSIs should be working to.
The current situation is creating 'complete confusion', he warned.
Dr Matthew Fay, a cardiology GPSI in West Yorkshire, said national guidance was crucial to embedding GPSIs in the NHS and expanding the roles they fulfil.
'If we are trying to set up a tier of general practice that is specialist GPs, we run the risk of running into the same problems as nurse practitioners did,' he said.
'Without a unified approach, we run a real risk of having a hotchpotch of services and creating an amorphous group.'
Dr Mark Dancy, who led development of the original accreditation process for GPSIs at NHS Improvement, believes any national guidance will have to explain how GPSI roles fit with the GMC's revalidation plans.
'There has got to be some process in place that assesses the specialist part of their roles,' he said.
A NHS Improvement spokeswoman said that, although the organisation had carried out work on GPSI accreditation in the past, it had no current plans to continue this work.