Minister for Health James Reilly has rejected calls for an independent inquiry to be carried out into the top-up controversy.
He also rejected claims by the Central Remedial Clinic that it had cut a deal with the Health Service Executive in 2009 to allow them to top up salaries.
Speaking on RTÉ’s News At One, Mr Reilly said he was deeply disturbed by the report that he commissioned last year which revealed the top-ups, but it was important to allow the process to conclude.
He said he was willing to cut funds so that those who are in breach of pay limits are hurt, but that services or the people who avail of services are not affected.
Yesterday, a former chairman of the CRC said there had been no misuse of funds at the charity.
Des Peelo said the HSE approached the organisation in 2009 and said that under new austerity measures, some CRC employees were being paid above the threshold.
Mr Peelo said there was no secret or hidden agenda and the agreement was made with the HSE in writing.
He said that money from fundraising efforts, such as the Santa Bear Appeal, was not used.
The HSE has denied that any breaches of the pay cap were sanctioned by the HSE.
Mr Reilly said he would fix the problem in the CRC and across all other agencies, but it cannot be resolved "at the drop of a hat".
He asked the public to trust in the fact that he will deal with the situation properly.
The minister said it was not fair that “front line staff are working so hard and that they’re fully compliant that others are not and we’re not going to tolerate that”.
Mr Reilly said there are people working in the Department of Health who were approved for higher salaries but they were granted permission to do so by the department and the Department of Public Expenditure and Reform after discussions with both departments.
In relation to the health service plan, Mr Reilly said it was still being worked on and it would not be seen until it was fit to be approved.
Charities need to be 'transparent' about donations
Tánaiste Eamon Gilmore has said charities need to be transparent about where public donations are going and reassure those making contributions that the money is going where it is intended.
Speaking in Dublin this morning Mr Gilmore said he was glad the CRC had made a statement on the issue of top-up pay for executives.
He also welcomed the institutions' willingness to co-operate with the Dáil Committee that would be looking at the issue.
Mr Gilmore said he now expects there will be discussion between the CRC and the HSE on the matter.
Complete transparency is needed, which is why the HSE has asked the agencies for information about whether they are complying with public pay policy, he added.
Earlier Sinn Féin called for an independent inquiry to be carried out into the ongoing top-up controversy.
Health Spokesperson Caoimhghín Ó Caoláin said there was a requirement to get to the full truth and that he did not believe an investigation by the Public Accounts Committee would go far enough.
Important that vital services not affected
Mr Ó Caoláin said he believed the problem went far beyond the Central Remedial Clinic and that the boards of all agencies should publish a full set of figures and accounts.
He said that it was important that vital services are not affected by the fall out and that the public continue to donate.
"I believe that all of these entities, each and every one of them not just the CRC, should in fact come clean.
"Their board should meet and they should publish the full details of the facts, and in relation to reserves that they're holding, because it is unnerving people.
"And I don't want to see a public reaction that in the end of the day those that are dependent on that charitable donation will lose out," he said.
Meanwhile, the head of a group that represents professional fundraisers has said there are no top-up payments in 95% of charities.
Fundraising Ireland Chief Executive Anne Hanniffy said yesterday the HSE paid the executive salaries of just a small number of charities.
But the rest relied totally on fundraising, so top-up payments were not an issue.
Last week, the CRC confirmed that some of the money donated by the public is being used to top up the salaries of some of its staff.
The funds were raised by a separate company called Friends and Supporters of the Central Remedial Clinic.
It admitted that the additional salary amounts were over the Department of Health's consolidated pay scales.
Ross says 'loan' really a gift
Meanwhile, independent TD Shane Ross has said a €3m loan from the Friends and Supporters of the Central Remedial Clinic to the CRC was a gift and not a loan, as claimed by the CRC.
Mr Ross cited the 2012 annual report of the Friends and Supporters' company.
He said the company's auditors said in that report that "provision has been made for the [€3m] amount due to the uncertainties regarding the long-term ability of CRC to repay the loan".
Mr Ross said this means that the money was a gift and not a loan.
He was speaking on RTÉ Today With Sean O'Rourke.
Yesterday, the CRC said that the €3m loan is expected to be repaid in full by 2017.
The CRC statement said it had been given by the Friends of the CRC to the clinic's pension scheme, which covers 70 former staff, in response to a requirement from the Irish Pension Board together with advice received from the CRC's pension advisers.