The Tánaiste and Minister for Health, Mary Harney, has said she is disappointed that some hospitals and consultants are not cooperating with the National Treatment Purchase Fund.
The fund was set up to treat patients who have been on waiting lists for long periods.
Speaking at the launch of the NTPF annual report, Ms Harney said there was now an obligation on the fund to work with the hospitals and consultants concerned to iron out the problems.
The minister Ms Harney said the fund must establish which hospitals and consultants in particular are not cooperating with it.
She warned the Government may have to look at changing the system to allow GPs refer out-patients directly to the fund.
The Irish Hospital Consultants Association said consultants were cooperating with the fund and that circumstances in a small number of cases may result in consultants not cooperating.