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AU said in a statement on Sunday that the funds of $2.98 million were originally part of a $10 million donation from Japan for this purpose.
The funds shall be administered by the Trust Fund for the Support of Lasting Peace in Darfur, said the statement.
According to UN figures, around 1.4 million remain homeless after the decade-long conflict.
El-Ghassim Wane, AU director of peace and security, and Mohamed Ibn Chambas, AU-UN joint special representative for Darfur, signed the deal at the AU headquarters on the sidelines of the celebrations of the 50th anniversary of the OAU/AU.
Since the initial deployment on Dec. 31, 2007, UNAMID is tasked with protecting civilians, contributing to security for humanitarian assistance and assisting an inclusive political process, among others.
In April, donor countries pledged $3.6 billion for the reconstruction of Darfur, which fell short of the $7.2 billion sought by aid organisations.
With inputs from Agencies