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
Humza Yousaf overruled officials in order to give £250,000 to a Gaza aid appeal as members of his family were trapped.
Government officials recommended a £100,000 to £200,000 donation to Unicef, the United Nations agency to help support water programmes in Gaza.
However, Yousaf announced that £250,000 of taxpayers’ money should instead be given to the United Nations Relief and Works Agency (UNRWA) - which has been criticised over claims it has links to Hamas.
He told officials that: "We should just announce an extra £250k to them".
The donation was publicly confirmed the same day that Yousaf met a delegation of senior UNRWA officials in Edinburgh on November 2.
A day later, on November 3, his mother-in-law and father-in-law left Gaza via the Rafah crossing.
The First Minister has rejected allegations that the donation was connected with the release of his family.
A spokesman said: "UNRWA had no role in the situation regarding the First Minister’s extended family, and any suggestion of a conflict of interest in this matter would be completely untrue."