A boat run by Spanish charity Open Arms that had been repeatedly denied permission to dock by both Italy and Malta was granted permission late on Saturday to enter the Sicilian port of Pozzallo.
Earlier on Saturday, the charity said it only had food for another two days as it remained stranded in the Mediteranean with 363 rescued migrants and refugees on board.
Italian media outlet Rai later reported that they would be distributed across the EU, as laid out in an EU agreement on settling migrants and refugees rescued in the Mediterranean.
In the past few months Italy has allowed such charity ships to disembark rescued migrants at its ports on condition that other European Union nations agree to take some of them in.
Several EU nations have done so, making good on pledges to share the migrant burden at a conference in Malta a few months ago.
During Italy's previous government, which included the anti-migrant League, then-Interior Minister Matteo Salvini triggered repeated standoffs at sea when he refused port permission to private rescue ships.
In some cases, the rescuers were left in limbo for days or forced to sail as far as Spain to disembark migrants.