The Health Service Executive is investigating pharmacists who have claimed payment for drugs that have not been dispensed to patients.
It is understood that several million euro is involved and the HSE is seeking repayment.
The medicines and products are provided under the State's primary care community drug schemes, like the medical card system.
HSE correspondence, seen by RTÉ News, says that a number of pharmacy inspections have highlighted that some pharmacies have not complied with the rules.
The executive wrote to over 1,700 pharmacies about the issue last month.
In the correspondence, it says that if agreement can be reached regarding recoupment of "invalid claims" and "voluntary disclosures" by pharmacists, the HSE will not initiate a disciplinary process, or legal proceedings.
Under the drug schemes, a pharmacist should only present a claim for reimbursement by the HSE, for items which have been supplied on foot of a prescription.
Difficulties can arise if the total quantity of medicines is not available at the time, or a patient does not return for a further quantity of medicines.
In some cases, a pharmacy will temporarily owe their patient a balancing quantity, for example where the total quantity of medicines is not available in the pharmacy at the time the initial prescription is presented.
Some pharmacists have charged the HSE for these drugs, according to the HSE.
The HSE says that a claim should only be submitted where the pharmacist has a genuine expectation that the patient will return to collect the remainder of their prescription.
In its letter to pharmacists, it has asked pharmacists to review their standard operating procedures, to establish if they have made claims for products not supplied to patients.
The Irish Pharmacy Union says pharmacies are subject to regular and ongoing inspection by the HSE and other State agencies.
It said that in the vast majority of cases no issues arise.
The IPU says the HSE acknowledges that "the vast majority of pharmacy claims are reasonable, valid and in compliance with contractual agreements in place".
The union says that to the extent that a small number of pharmacies may have submitted inappropriate claims, the IPU has cooperated with the HSE on a mechanism to regularise their position.
Speaking on RTÉ's News at One, IPU Secretary General Darragh O'Loughlin said he cannot comment on the figure of several million euro as the HSE has not issued a statement in relation to how much money is believed to be involved.