Minister for Media Catherine Martin has said she is disappointed that the RTÉ Executive Board decided to increase members' pay by 10%, at a time she was negotiating interim funding for the organisation.
Ms Martin said while matters of pay are not under her remit, she understood the frustration of staff in relation to the matter.
She said the matter of pay was one for RTÉ and it was not the place of the Government to "micro-manage at that level".
However, Ms Martin said she had raised the issue of executive pay with RTÉ during the summer and would continue to do so.
Earlier, Taoiseach Leo Varadkar said he does not believe executives at RTÉ should have to pay back the pay increase.
The salary increase for members of the Executive Board came in the form of a restoration of a previous pay cut. The pay restoration took effect last September.
Mr Varadkar acknowledged that it was "very annoying" for the public and staff at RTÉ to learn that what had been presented as a pay cut was only for a year.
But, asked directly if the money should be paid back, he said: "I don't believe so - that really is a matter for the individuals involved."
Mr Varadkar said the Government has a role in determining pay in its departments and in State agencies, but it did not have a role in determining pay at State-owned enterprises, such as RTÉ and the ESB.
"What is very annoying for people certainly and for a lot of the rank and file staff in RTÉ is that what had been presented as a pay cut was really only a one-year pay cut, a one-off pay cut," Mr Varadkar said.
"That has certainly caused a lot of annoyance, particularly for the regular staff in RTÉ who would have thought otherwise."
However, he added: "We are not going to be - from Government - trying to impose pay cuts on other people.
"(RTÉ) is a State-owned enterprise and it runs its own affairs."
Mr Varadkar reiterated that RTÉ needed to produce a new financial plan and a reform plan.
"Any additional funding this year and next year will be conditional on that," he said.
In a statement this afternoon, RTÉ Director General Kevin Bakhurst said he was committing that "there will be complete transparency around the pay of the new leadership team at RTÉ."
He added: "I have already said that we will publish their pay annually in the RTÉ Annual Report, and we will do so. Transparency and accountability to the audience and to the Oireachtas will be critical.
"I aim to deliver that transparency in the changes that we have made and in the plans we will outline in the weeks ahead for a new and more open RTÉ."
Earlier this week, Mr Varadkar said no additional funds would be provided until the Cabinet has assessed the broadcaster's reform plan which is due in October.
Mr Varadkar's comments came after RTÉ confirmed that it wrote to Minister for Media Catherine Martin again last week seeking €34.5m in interim funding, following a previous request for the same amount submitted in May.
Any increased funding to RTÉ must be "conditional" on changes and on radical reforms, Labour Party leaver Ivana Bacik has said.
Speaking on RTÉ's Today with Claire Byrne, Ms Bacik said she was shocked and very surprised to hear that the 10% pay cut to the salaries of top executives was restored last year.
She said: "I think the crucial thing here is to ensure that those who have been paid the least, whose position has been most undermined by RTÉ failing to recognise them as employees, I think it should start there."
