Minister for Health Simon Harris has said he is disappointed that the latest NTPF waiting list figures for January show an increase.
However, he promised that by the end of the year, people will be waiting less time for procedures.
He was speaking during a Dáil debate on waiting lists following Monday night's RTÉ Investigates 'Living on the list' programme.
Mr Harris said the problems in the health service were not just about resources, but it was about how money is spent and how hospitals are managed.
He said increased funding needed to be under pinned by tougher accountability rules.
"We have excellent management in the health services but there's room to do more," he said.
He also rejected that there is "no room for improvement" on how the health service is managed and said party politics should not be played when it comes to the health service.
Fianna Fáil health spokesperson Billy Kelleher said the Government should not be surprised at the rise in waiting lists because the only "safety valve" - the NTPF function of hospital treatment provision - was scrapped in 2011.
He said the minister was like a "nasty jockey on a very tired horse" criticising the Health Service Executive.
Mr Kelleher asked if the minister had confidence in HSE Director General Tony O' Brien.
Mr Harris said he did have confidence in Mr O'Brien, but did not have blind confidence in everyone.
Mr Harris also said he will have an action plan for scoliosis by the end of the month and Mr O'Brien had committed that by the end of this year, no child would wait loner than four months for a pediatric scoliosis target, which he described as an ambitious and bold target.
Sinn Féin leader Gerry Adams called for a single integrated waiting list.
He raised the case of a female law student from Letterkenny, who he said needs an ENT procedure and has no date for the procedure and who has also been on an orthopaedic waiting list for four years.
Sinn Féin health spokesperson Louise O'Reilly said Fine Gael had promised to tackle waiting lists and to make sure the figures were accurate.
She said there had been a fundamental change in what is published by the NTPF.
Meanwhile, the HSE says it plans to develop Our Lady's Hospital Cashel into a community service, including a day hospital, assessment service and more care of older people.
Mr Harris and Labour health spokesperson Alan Kelly visited the hospital late last year and found it had no patients.
The former 40-bed facility was recently refurbished at a cost of millions of euro and was referred to in the Dáil as being like a scene from an episode of TV programme 'Yes Minister'.
In the Dáil last month, the minister said the visit was etched on his mind because he saw a beautiful facility not being fully utilised.
Mr Kelly described it as a "phantom hospital".
The HSE said today that currently services include minor injury diagnostics and primary care.
Acute services are not expected to return to the facility, which does not provide for overnight stays.
The Public Accounts Committee is expected to examine the use of public money in renovating the facility amid reports that the refurbishment ran about €7m over budget.