The HSE has asked the Garda to carry out an investigation into what happened to €2.35 million allocated for a staff training programme over recent years.
The move follows an internal audit carried out within the HSE over recent months.
However, last night Siptu said in a statement that it had not received any of the money concerned.
The Sunday Timesyesterday reported an extract from the HSE's forthcoming annual report, to be published next week, in which chairman Liam Downey states: "The audit identified weaknesses in governance, control of and accountability for funds disbursed in respect of administration of the programme.
“In particular, the audit review identified payments of €2.35 million to one organisation over the period 2002 to 2009 not accompanied by adequate supporting documentation. All payments to that organisation have ceased since November 2009.”
However, a spokesman for Siptu last night denied the trade union was the “organisation” referred to.
The newspaper maintained that HSE auditors had raised concerns about foreign trips, airline flights, taxi journeys, meals and other expenditure over a five-year period from 2004.
“Siptu can categorically state that it has not received from either the Department of Health or the Health Service Executive any of the reported €2.35 million in payments made for the health care staff training programme.
“Siptu informed the HSE of this fact in correspondence when first contacted by the agency in October 2009,” the union stated.
Siptu said that it was aware the HSE was conducting an audit over the training programme and that it had co-operated fully with the investigation.
“Siptu has not been made aware by the HSE or any other agency of any further concerns it has in relation to this matter or of any referral, as reported, to the Garda Síochána,” the union said in a statement.
The HSE said yesterday that it could not comment as the matter had been referred to the Garda.
The newspaper maintained a training programme for around 2,000 staff annually in non-clinical, non-administrative areas had been set up under an agreement a number of years ago between Siptu and the HSE.
It said the programme had received about €60 million in funding between 2003 and 2008.