The Higher Education Authority has confirmed that it knew extra payments were made to the two presidents of NUI Galway and UCD.
The HEA said it's been in discussions with the Department of Education and the two universities over the payment of allowances outside the national pay policy.
Extra allowances are not permitted under this pay policy, unless approved by the Ministers for Education and Finance.
A pay freeze has now been imposed until the payments are withdrawn, and an investigation is expected.
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