Health minister Nicola Blackwood told parliament last year that she had 'made it clear to Capita that I expect it to consider compensation as an option' for practices hit by problems with the service it delivered.
GPC chair Dr Chaand Nagpaul also wrote to NHS England in November to demand immediate compensation for practices that had not received thousands of pounds in trainee reimbursements due to them, and advised practices to take legal action to claim the funds.
Her warning came after a string of concerns with the service. An official user survey published in October found that four in five GPs were not satisfied with the service, following BMA warnings that problems with delayed transfer of patient records, delayed delivery of prescription pads and other items had left patients at risk.
Practices have also reported problems with late or incorrect payments, which could trigger bank charges if short-term cashflow issues push practices past overdraft limits.
An NHS England spokeswoman said: 'NHS England is conscious that concerns have been raised about costs and extra workload on some practices as a result of these issues. Representative bodies have raised this with us and we are considering what we could put in place to support those practices that are most affected.'
GPC deputy chair Dr Richard Vautrey told GPonline: 'Those individuals and practices that have lost out because of Capita's failure deserve compensation and this is certainly something we are pushing for.
'Practices that have incurred a demonstrable loss have a right to expect to be compensated, so for instance practices that might have incurred bank charges as a result of late payments.'
Capita directed queries on possible compensation back to NHS England, but has previously apologised for problems with primary care support. A spokesman said last year: 'NHS England contracted Capita to both streamline delivery of GP support services and make significant cost savings across what was a highly localised service with unstandardised, generally unmeasured and in some cases, uncompliant processes. We have taken on this challenging initiative and we have openly apologised for the varied level of service experienced by some service users.'