The Irish Hospital Consultants Association has criticised the Government for failing to meet its waiting list targets under the National Health Strategy.
It was responding to a report by the National Treatment Purchase Fund, which showed that almost 5,000 patients are on waiting lists for surgery at seven of the country's major hospitals.
The Minister for Health, Tánaiste Mary Harney, earlier defended the Government's performance, saying that the overall number of people waiting for surgery had decreased over the years.
But the IHCA said comparisons with previous waiting list figures were meaningless, because the system used for today's report differed from previous surveys.
The figures released today showed that there are almost 5,000 patients on surgery waiting lists at seven of the country's major hospitals. 1,000 of these have been waiting for over 12 months.
Ms Harney said the overall number of people waiting for surgery has steadily decreased from 39,000 in the 1990s to around 10,000 people now.
The Patient Treatment Register shows that at six Dublin hospitals and one in Limerick, there are 4,944 patients waiting for a surgical procedure.
The National Treatment Purchase Fund, which is responsible for operating the new register, said waiting times have significantly reduced in the seven hospitals on the register and that for the most common surgical procedures, patients are waiting two to four months for an operation.
The new system will provide patients and GPs with website access to live waiting list data.
In future, when patients are placed on the Patient Treatment Register, after being referred for treatment by a consultant, they will be given a treatment card so their waiting time can be tracked.