Minister for Health James Reilly told the Dáil that he was pleased to be able to improve facilities at St Luke's Hospital in Kilkenny and Wexford General Hospital as both projects had been planned for a long time.
Minister Reilly said he is taking a hands-on approach to getting waiting lists in hospitals to fall.
He said there has been a decrease in waiting times and the number of people on waiting lists since he took office.
The minister said he visited the Wexford hospital and was taken back by what he saw.
He said he approved a new patient assessement area in St Luke's Hospital that was needed.
These projects, he addded, are part of capital plans by the HSE and he was pleased that he had the €12m to do it.
Mr Reilly rejected a suggestion that it will delay a new unit in Roscommon.
Responding to the minister, Fianna Fáil’s health spokesperson Billy Kelleher said that he had no problem with Kilkenny and Wexford getting the improvements, but that Minister Reilly had interfered.
People Before Profit Alliance TD Richard Boyd Barrett said there should be transparency when it comes to allocating resources and he accused the minister of engaging in "cute hoor" politics.
Sinn Fein's health spokesperson Caoimhghín Ó Caoláin said the minister was trying to get away from the core issue of what talks went on between Minister for Public Expenditure and Reform Brendan Howlin and Minister for the Environment Phil Hogan.
The Cabinet did not discuss the controversy over the fast-tracking of the hospital projects.
Yesterday, Minister for Education Ruairi Quinn said he was sure the matter would be discussed and all the details given by Mr Reilly.
A Government spokesperson said the two ministers spoke about the issue after today's Cabinet meeting.
Earlier, Sinn Féin leader Gerry Adams accused the Government of lacking transparency over the decisions made by Fine Gael and Labour ministers.
In the Dáil, Mr Adams asked Taoiseach Enda Kenny about hospital upgrades being announced without reference to the Health Service Executive.
Documents released under freedom of information to RTÉ’s This Week show that Mr Reilly told the HSE to accelerate hospital projects at St Luke's and Wexford.
Local ministers made announcements about the work before the HSE Board became aware of the change.
Mr Adams said the decisions about the two hospitals were revealed only by journalists.
Mr Kenny told the Dáil that the two hospital projects had been in progress since 2006.
He said the capital allocation budget had been cut in 2009 and that the reality was that the projects were paused.
Mr Kenny said some projects in the south were delivered under budget in 2011 and that allowed the Kilkenny project to get extra money.