Revalidation is on track to begin in December, but RCGP revalidation lead Professor Nigel Sparrow told GP that in parts of the UK, NHS organisations allow the same official to investigate and assess concerns raised about doctors.
Professor Sparrow warned the two stages must be 'completely separate' to guarantee fair handling of complaints.
The RCGP has developed standards for investigation and management of concerns about GP performance by primary care organisations (PCOs) in a bid to tackle the concerns.
Professor Sparrow said: 'We are aware there is tremendous variability in the way GPs are investigated. The college wanted to set standards for the initial assessment and investigation. Investigation needs to be separate from assessment.'
He said the guidelines for investigating complaints should help to standardise remediation for GPs, in the run-up to revalidation.
A report from the Academy of Medical Royal Colleges, which revealed the RCGP proposal to standardise guidance, says PCOs should consider paying royal colleges to support doctors' remediation.
In the past, when concerns about a practice or GP did not require a GMC referral, PCOs sought help from postgraduate deaneries, LMCs or a professional support unit, the academy said. It said the RCGP could play a more active role in supporting GPs who are the subject of 'low-level concerns'.
Professor Sparrow warned that concerns remained about variation in appraisal. In some areas, GPs were being told they had to achieve a specified piece of training to be revalidated, when this was not required.
'Some PCTs are asking for child protection training - a specific programme that isn't required for revalidation,' he said.
GPC deputy chairman Dr Richard Vautrey said: 'There has been variation in the way PCTs have dealt with performance issues. It is one of the roles of the RCGP to set appropriate standards and we work closely with them on this.
'It is important to do this as we move to one NHS Commissioning Board, to use this opportunity to ensure that wherever a doctor works, they can expect to be treated in the same way using the same standards.'