Minors and the sick were let off the German-flagged Humanity 1 in the early hours at the port of Catania, but 35 adult male migrants were refused permission to set foot on Italian soil, charity SOS Humanity said.
A total of 144 people disembarked.
Fellow humanitarian vessel Geo Barents, run by Doctors Without Borders' and sailing under a Norwegian flag, said it too has been summoned so authorities could "evaluate vulnerable cases" among the 572 rescued people on board.
Interior Minister Matteo Piantedosi earlier said those who do not "qualify" would have to "leave territorial waters", after refusing requests by four charity vessels for a safe port.
The Geo Barents, Ocean Viking and Rise Above are still carrying 900 migrants between them.
Italy's new far-right government, which was sworn in last month, has vowed to crack down on boat migrants attempting the perilous crossing from North Africa to Europe.
Over 87,000 people have landed in Italy so far this year, according to the interior ministry -- though only 14 percent of those were rescued at sea and brought to safety by charity vessels.
Sources close to far-right transport minister Matteo Salvini, who controls the ports, said Sunday the Geo Barents was only being allowed in temporarily.
"Those who remain on the vessel will be provided with the assistance necessary to leave territorial waters," the sources said.
'Extremely depressed'
The 35 migrants refused permission to leave the Humanity 1 were "extremely depressed", SOS Humanity's press officer Petra Krischok told AFP.
It was not clear whether the ship would be ordered to leave.
"For now, we stay here and wait," she said.
The leader of the main opposition party, Democratic Party chief Enrico Letta, accused the government on Twitter of breaking international law.
Il #caricoresiduale e lo #sbarcoselettivo. Linguaggio inaccettabile per scelte a #Catania ancor più inaccettabili, contrarie ai principi di umanità e alle regole internazionali. #Humanity1
— Enrico Letta (@EnricoLetta) November 6, 2022
Piantedosi should explain his actions to parliament, the party said.
Member of parliament Aboubakar Soumahoro, present as those chosen from the Humanity 1 were disembarked, slammed the "selection of shipwrecked migrants".
Un naufrago si è sentito male e non c'è neanche un'ambulanza sul posto. Pres. @GiorgiaMeloni lei ha la responsabilità di ogni vita attualmente sospesa sulla nave @soshumanity_de al porto di Catania. Non potete piegare la vita di esseri umani a convenienze di Palazzo. Resistenza! pic.twitter.com/muyoJ2cUAq
— Aboubakar Soumahoro (@aboubakar_soum) November 6, 2022
He said far-right Prime Minister Giorgia Meloni's government was treating "the worn-out bodies of shipwrecked people, already exhausted by cold, fatigue, trauma and torture... as objects".
"If the remaining castaways are rejected... we will challenge this decision in all appropriate institutions," he said on Twitter.
'No responsibility'
Piantedosi said Saturday those migrants not allowed to disembark would have to be "taken care of by the flag state" -- a reference to the national flags under which the vessels sail.
The Humanity 1 and Mission Lifeline charity's Rise Above sail under the German flag.
The Geo Barents and SOS Mediterranee's Ocean Viking are registered in Norway.
The Norwegian foreign ministry said Thursday it bore "no responsibility" for those rescued by private Norwegian-flagged ships in the Mediterranean.
Germany insisted in a diplomatic "note" to Italy that the charities were "making an important contribution to saving human lives" and asked Rome "to help them as soon as possible".
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