The HSE withheld payment on almost 63,000 claims by family doctors for out-of-hours work after identifying claiming patterns of concern, it says.
The review was carried out as part of routine probity and audit measures in 2009 and resulted in the HSE being unable to verify the reasonableness and accuracy of some claims, according to a spokeswoman.
After discussions with the Irish Medical Organisation, the two sides entered into a binding arbitration process to resolve the unpaid claims.
Claims submitted
The HSE says it received almost 441,000 out-of-hours claims submitted by 264 doctors between February 2011 and July 2013.
Of these, payment was withheld in respect of 62,966 claims.
Under the mediation agreement, the HSE paid 211 GPs the full amount of their unpaid claims, amounting to €537,000. A partial payment was offered to the remaining 53 GPs, totalling €377,204 in respect of 28,543 claims.
In one case, a doctor who claimed €186,000 in back fees was offered a settlement of €15,000.
GPs have until the end of October to accept the settlement offer or exercise their right to appeal. The IMO said the vast majority of the 2,200 GPs in the scheme and providing out-of-hours services were not in dispute with the HSE over payments.