Dee Forbes, the director general of RTÉ, has resigned effective right away.
Presenter Ryan Tubridy received €345,000 (£296,800) more than what was disclosed in the Irish broadcaster's earnings reports at the time of the move.
The payments were made between 2017 and 2022 to the TV and radio host.
According to a statement released by Ms. Forbes on Monday, she has "engaged with and consistently cooperated with the processes directed toward answering questions surrounding payments to Ryan Tubridy.".
She continued, "As director general, I am ultimately responsible for what occurs within the organization, and I take that responsibility seriously.
"I am resigning from RTÉ effective immediately. ".
The Late Late Show, Ireland's longest-running TV chat show, was hosted by Mr. Tubridy until he recently announced his resignation. Northern Ireland comedian Patrick Kielty was named as Mr. Tubridy's replacement.
On Wednesday, the Irish broadcaster has been asked to testify before the Oireachtas (Irish Parliament) media committee.
A second appearance before the public accounts committee will come after this on Thursday.
Additionally, corporate governance at the station will be subject to an impartial external review.
The National Union of Journalists (NUJ) at RTÉ applauded the announcement and insisted that any review be done promptly and in a transparent manner.