The Dáil approved the increase last week.
The three Super Junior Ministers have agreed to give back the €16,000 in extra salary the Dáil approved for them last week.
Instead Offaly's Pippa Hackett, Jack Chambers and Hildegarde Naughten will split the two existing allowances and will get a wage increase of a little over €10,000 each.
Ministers have also agreed to take an across the board 10 per cent pay cut.
However, many will still earn slightly more than the last government which had turned down incremental increases in their wages.