It has emerged that the Government has not made any application for European Social Funds for FÁS for almost ten months.
Following an EU audit last November, the European Commission said that, in order to protect taxpayers, it wanted issues to be resolved before further funds were requested or paid.
RTÉ News has learned that the problems relate to training courses carried out by private operators.
The European Commission is reviewing some of the €600m allocated to FÁS in the last ten years.
Under the European Social Fund 'human capital investment programme' 2007-2013, FÁS has been allocated €211m in funding for training and education.
This fund is one of the main sources of EU funding for FÁS.
The European Commission has confirmed to RTÉ that no applications have been made by Irish authorities since November 2009.
The European Commission is now reviewing previous applications to FÁS for a programme which ran between 2000-2006 as €407m was allocated for this period.
The commission has said that 'it is in the interest of the Irish authorities and the commission to sort out any unclear issues before money is requested and paid to ensure there is no risk or damage to EU taxpayers'.
The commission has said that the Irish authorities have until the end of this month to respond to their queries.
It added that it was too early to say if money will have to be returned.
The Department of Education, which has responsibility for FÁS, has said that it has until 2017 to make application for ESF funds.
The Department continued it never anticipated applying for the funds this year and it has nothing to do with the audit.
FÁS is due back on the agenda of the Public Accounts Committee in the coming months.
Chairman of the PAC Bernard Allen has said that the development was extremely disturbing.
He added it was strange that funding applications were not being made at a time when there is huge demand for FÁS courses and the Exchequer is under pressure.