The Department of Public Expenditure and Reform has confirmed that the Minister for Employment Affairs and Social Protection Regina Doherty will have to pay back an allowance of almost €16,000 that she had received while she was Government chief whip.
The announcement follows advice from the Attorney General.
A spokesperson for the Department of Public Expenditure and Reform said the advice outlined that a decision taken by the department to pay the allowance to Ms Doherty had no legal basis.
In June, Labour leader Brendan Howlin asked newly-elected Taoiseach Leo Varadkar about the legality of the annual allowance paid to the former government chief whip and "super junior" minister.
Mr Howlin told the Dáil that the legislation only allows for such "top-up" payments to two super junior ministers and in the previous government Finian McGrath, Paul Kehoe and Ms Doherty were receiving the allowance.
There are currently three super junior ministers: Mr McGrath, Mr Kehoe and Mary Mitchell O'Connor.
Ms O'Connor has not received the additional allowance.
Legislation would be required for her to receive it and Minister for Finance and Public Expenditure and Reform Paschal Donohoe has indicated the legislation is not a priority.