There have been calls in the Dáil for Minister for Health Simon Harris to ensure a proper auditing system in the Health Service Executive.
Fianna Fáil's private members' motion calls for clarification on the action the HSE is taking to investigate incorrectly claimed pharmacy fees.
Fianna Fáil Health Spokesperson Billy Kelleher said a robust internal auditing system of the HSE needed to be put in place, stressing the importance of getting value for money for the taxpayer.
Fianna Fáil TD Dara Calleary asked Minister Harris what work was under way in his department to ensure that checks and balances are under way in the HSE.
The deputies pointed out that the matter was revealed by the RTÉ Investigations Unit.
The minister said that the Government is not opposing the motion, however said that "a number of points need to be appreciated".
Minister Harris said he had been briefed in detail by the HSE on the matter.
He said in 2014 a HSE data review of phased dispensing raised concerns about activity and claiming levels, and in early 2015 the HSE began investigating claiming by the Lloyds pharmacy group.
Mr Harris pointed out that the investigation involved complex analysis of activity for the period from 2010 to 2015, and detailed pharmacy inspections.
He said the HSE considered the Lloyds agreement to a settlement that included full repayment of over-claimed fees was the best possible outcome in this case, with full return of moneys owed.
The minister said the Primary Care Reimbursement Service (PCRS) is also examining other claiming issues and is conducting investigations into claiming by a number of other contractors.
Mr Harris also noted that the PCRS has appointed four full-time pharmacy inspectors, two data analysts and two dedicated case managers.
A third data analyst and two more case managers are being recruited, he said.
The minister said he would not accept the proposed Sinn Féin amendment on two other issues: reclassifying medicines to over the counter and transparency in pharmacy prices and services.
He said the issues are the responsibility of the relevant statutory authorities - the Health Products Regulatory Authority for medicine classification and the Pharmaceutical Society of Ireland for professional practice and conduct.
Fianna Fáil TD Robert Troy said it is "alarming" that there was an awareness within the HSE of irregularities in relation to prescription charges but nothing was done about it.
He asked if there will be an investigation into contracts awarded by the HSE throughout the country to ensure taxpayers are getting value for money.
Mr Troy said that if somebody passes away and their home help hours are reallocated, only 25% of those hours are reallocated.
He said home help hours have been slashed in 2016 so the €12m lost in pharmacy fees could have helped to alleviate this situation.
The debate on FIanna Fáil motion has now concluded and it will be voted on on Thursday.