Around €2.7 million in taxpayer's money was provided to a private company run by the country's biggest doctors' trade union, the Irish Medical Organisation.
Documents secured by RTÉ News under the Freedom of Information Act show that the company, called Irish Medical Educational Services Limited, received the funds from State drug savings between November 2001 and December 2005.
The savings arose from GPs prescribing more carefully and also using more generic drugs.
IMES was set up by the union for the education and training of doctors.
The State funding was used for information technology, the development of GP training programmes, rural practices and other services.
RTE News has learned that in recent days the IMO returned €126,000 of public funding to the HSE after the executive raised queries in January as to whether any State funds were still held by IMES.
In November 2014, RTE News first sought details about the funding provided by the State to IMES as part of a Freedom of Information request.
Around 28 documents were released by the HSE in the public interest.
The IMO has objected to the release of 12 other documents and the issue is with the Information Commissioner for a decision.
The union insisted that the material was provided in confidence, that its release would breach an agreement with the HSE and that the documents contained commercially sensitive information.
The invoices for funding the IMES released under the FoI Act do not give the names of doctors, or any others who received payments.
It has been confirmed that the State did not conduct any value for money audit on the funding provided to the union.
The funds were provided by precursor agencies to the HSE, namely the then GMS Payments Board and payments were also approved by the Department of Health at the time.
The funding came from the former Indicative Drug Target Savings Scheme, under which savings from drug prescribing by GPs could be reinvested in general practice.
Correspondence released by the HSE shows that it wrote to the IMO's Chief Operations Officer, Susan Clyne, on 21 January on whether any public monies were still held by it.
In June, it wrote to the President of the IMO, Dr John Duddy saying it was 'critically important' that it receive the information sought.
The primary source of income for IMES was taxpayer's money and its latest accounts for 2014 show that it retained assets of €125,000.
Drug savings funding ceased in 2005 and since 2008 the IMES has been effectively dormant with no employees.
In its letter to the IMO in January, the HSE noted that IMES was still a registered company and still held 'a substantial cash balance'.
The HSE also noted that the balances were reduced as a result of substantial payments made by the company between 2011-13 "in legal and administrative fees, and travel costs"
In a statement, the IMO said the objective of the scheme under which the IMES was funded was to lower the cost to the State of prescription medicines.
When it ceased to operate in 2005, there was residual funding in IMES which continued to be used for projects to support the aims of the original agreement.
It said the remaining funds left in the company have been returned to the HSE as they had not been spent and all the initiatives had ceased.
The IMO said that no legal costs were incurred and no payments for legal costs were made by IMES between 2011 and 2013.
