The review was announced in a letter sent on Thursday to all GPs in the NHS pension scheme by NHS England and the NHS Business Services Authority (NHS BSA), which administers health service pensions.
The letter says: 'As part of NHS England’s quality assurance of the pension scheme records, a small sample review has been carried out which has shown discrepancies between some of the pensionable earnings and contributions data which has been provided to NHS BSA.
'We would like to assure you that your pension entitlement is safe. Our priority is to ensure that where there are any discrepancies, they are identified and resolved as quickly as possible.'
Since September 2015, Capita - the private outsourcing giant that runs NHS primary care support services - has been responsible for the administration of GP pension contributions.
BMA leaders hit out at Capita's management of NHS pensions earlier this year, warning that delayed pension payments to retiring GPs had left some 'facing the prospect of hardship'.
The letter setting out plans for the review warned it 'may take some time to complete'. It said: 'We will prioritise the records of any GPs who are nearing retirement age (56 or over), GPs who have recently retired and GPs who have died in service.'
GPC chair Dr Richard Vautrey told GPonline: 'We have been in discussions with NHS England and this letter is in response to that. They have assured us that no GP will lose out and all will get the correct pension.'
Lizzy Lloyd, a board member of the Association of Independent Specialist Medical Accountants (AISMA), said: 'This has come as no surprise to accountants dealing with the fall-out from Capita's mishandling of GP pension contributions since September 2015.
'All GPs will be concerned but locums are particularly worried about the data discrepancies since they have no way of checking whether the pension payments they submit to Primary Care Support England (PCSE) each month are received.
'Even when total reward statements are available from NHS Pensions they are often inaccurate and GPs should get them checked by a specialist financial adviser or accountant who understands the scheme.'
NHS England said that GPs with discrepancies in their pension data would be contacted directly. A spokesperson said: 'An independent expert has been appointed who is working with NHS England, Capita and the NHSBSA to look at the detail of this and tackling any discrepancies. We are contacting GPs and helping resolve any issues.'
Capita has previously suggested that any problems with pension payments to GPs may result from incomplete data being supplied to its primary care support team.
A spokesperson said earlier this year: 'Only when applications have been approved can they be sent to NHS Pensions for processing. Incomplete or missing documents can result in a delay to pension applications being approved and processed. We work directly with GPs where incomplete applications are received.’