The agency nurses and care assistants are owed eight months of back pay starting from December 2011 and have now been told that it will be early next year before they get it.
One care assistant who works in a Dublin hospital and is on a salary of €22,000 told how she is owed €3,000.
The Temporary Agency Work Act was introduced this year and since July agency staff have been paid the same as directly employed workers doing the same job. Under the act, payments are backdated to December 5, 2011, meaning that hundreds of agency staff are due to share in a €2.5m bonanza.
However, they have yet to receive their money.
The HSE said hospitals and agency CPL Healthcare are still trawling through files to calculate and verify each agency employee's hours worked. The back pay is not due to be paid until early next year.
A spokeswoman said that the agencies are required to provide details to the HSE regarding the hours worked by each agency staff member for the period December 5, 2011 to July 30, 2012.
"These details need to be verified with the service (eg hospital) concerned before payment can be made by the agency to the staff member," said the HSE spokeswoman.
"This detailed piece of work, that requires validation by both CPL Healthcare and the HSE, is ongoing and it is anticipated that, once completed, retrospective payments will be made in early 2013."
She said the HSE had committed to meeting its obligations under the act and all agency staff contracted by the HSE were currently being paid the correct incremental scale.
A spokesman for CPL said it had no comment to make but any staff members concerned about back pay could contact it.
The Irish Nurses and Midwives Organisation has claimed agency nurses have been effectively paid between 18pc and 25pc less than HSE nurses since March last year.
The HSE has estimated that the new pay rates for agency staff will cost an extra €30m a year.
This will wipe out much of the savings it made when it renegotiated contracts with recruitment agencies, which was due to save about €45m a year.