Hospitals have been warned by the Minister for Health that they risk a reduction in their waiting-list funding if they do not meet agreed targets to cut waiting times for procedures for public patients.
But Mr Cowen promised more funding for waiting lists "to reward those hospitals which are performing best and achieving or exceeding the targets in their service plan".
Mr Cowen also warned that hospitals would not get funding for waiting lists, if they did not provide information on time for his Department.
He told deputies there was "a need to get more information quickly".
He told Fine Gael's health spokesman, Mr Alan Shatter, that at the end of December about 36,883 people were on hospital waiting lists. Of these 1,156 adults and 73 children were waiting for cardiac surgery. A further 3,111 people were waiting for cataract operations, while 1,590 patients were on the list for hip replacements.
Funding alone was not the solution, he said. Even though they had increased funding by £4 million, or 50 per cent, from £8 million to £12 million, the lists went up by about 3,000.
He said the report of the Review Group on the Waiting List Initiative recommended the introduction of "positive financial incentives to hospitals to reduce waiting times".
He had therefore decided to retain some of the funding available for Waiting List Initiative Work and to redistribute it to those hospitals showing "the most progress in reducing their average waiting times".