The National Association of General Practitioners says it has been warned that the Competition and Consumer Protection Commission is monitoring the organisation.
It follows the decision by one of its members to take a High Court challenge over the introduction of free GP care for children under 6.
Dr Yvonne Williams, from Shannon in Co Clare, claims the scheme places her in an impossible position and could jeopardise her practice.
The representative body for GPs says it does not believe the CCPC needs to intervene in its dispute with the HSE over patient care.