The Alan Kurdi, a boat run by the German charity Sea-Eye, docked Sunday at the Italian port of Taranto, allowing 88 migrants it rescued more than a week ago to disembark.
The vessel arrived shortly before 9 am (0800 GMT).
‘We're overjoyed to know that Captain Baerbel Beuse, the crew and the rescued are finally safe,’ Sea-Eye tweeted.
Before the migrants disembarked, doctors came on board and found no one in need of urgent medical attention, Sea-Eye spokesman Gorden Isler told dpa.
One of the migrants knelt and kissed the ground as he got off the boat, the ANSA news agency said.
‘The migrants luckily are all fine. There are five unaccompanied minors and one woman among them,’ Taranto's council member for welfare, Gabriella Ficocelli, told ANSA.
She said they were taken to a reception centre and would be relocated within 36 hours. ‘We saw big smiles on their faces, they couldn't wait to get off,’ Ficocelli added.
Isler said the Alan Kurdi would have a technical stopover in Taranto for a few days and resume operations with a new crew in a week's time.
The German vessel picked up the migrants on October 26 off Libyan shores. At the time, Sea-Eye accused Libyan coastguard officials of disturbing the rescue by firing warning shots into the air and water.
Sea-Eye had to wait until late on Friday to get authorisation from the Italian Interior Ministry to reach an Italian port, and it only came after other EU countries agreed to take some of the migrants.
The ministry said more than two-thirds of them would be relocated: France and Germany are to take 60, Portugal five and Ireland two.
Earlier Friday, the Alan Kurdi entered Italian waters without authorisation, saying it needed to go closer to the shore to protect itself from bad weather.
Meanwhile, some 151 migrants disembarked from the Asso Trenta, an Italian cargo ship, after it docked in the Sicilian port of Pozzallo, ANSA said.
The migrants, also fleeing from Libya, were rescued between late Friday and early Saturday, according to the Alarm Phone charity, which initially spoke of around 200 rescuees.
Italy and Malta usually refuse to open their ports to charity rescue vessels unless other EU countries agree to take in some of the migrants.
The negotiation of burden-sharing arrangements is time-consuming and leaves migrants stranded at sea until a deal is struck. The process is normally coordinated by the European Commission.
In September, Malta, Italy, France and Germany suggested fixed rules for migrant relocations, to speed up procedures, but the proposal has failed to win wider EU endorsement.
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