The Norway-flagged Geo Barents, carrying 572 migrants, arrived in Catania on Sunday afternoon.
Migrants on board cheered as the ship entered the port and later the Red Cross brought food and water to the ship.
Authorities inspected migrants aboard the ship and allowed minors, families, and people with medical issues to disembark.
A spokesman on board the ship said they were waiting for further instructions from Italian authorities.
"At the moment the people that is remaining behind without disembarkation, we don't know what is going to happen. We haven't received any further instructions to what is the situation with them," said Lucia Blanco Soto, Deputy Project Coordinator of Medecins Sans Frontieres.
Lucia Blanco Soto said she was unsure what would happen to the remaining migrants.
"We haven't received any further instructions to what is the situation with them," she said.
Omar, a Syrian migrant who disembarked the ship, thanked the crew and the country for supporting him.
"Thank you for everybody in this great ship, for the team, the great team, they are caring us, they are doing the best in 24 hours, thank you. God bless you."
Italian Premier Giorgia Meloni's two-week-old government is refusing safe port to four ships operating in the central Mediterranean that have rescued migrants in distress, and is allowing only those identified as vulnerable to disembark.
Two other ships carrying rescued migrants remained at sea.
The charity ships say the rescued migrants are sleeping on floors and decks, spreading respiratory infections and scabies as food and medical supplies are nearing depletion.
Some migrants have been on the ships for more than two weeks.
The German-run Rise Above, carrying 93 rescued at sea, sought a more protected position east of Sicily due to the weather, but spokeswoman Hermine Poschmann said Sunday that the crew had not received any communication from Italian authorities.
Poschmann described cramped conditions on the relatively small 25-meter (82-foot)ship.
The Ocean Viking, operated by the European charity SOS Mediteranee, with 234 migrants on board, remained in international waters, south of the Strait of Messina, and did not receive instructions to proceed to a port, a spokesman said Sunday.
Its first rescue was 16 days ago.
The confrontational stance taken by Meloni's government is reminiscent of the standoffs orchestrated by Matteo Salvini, now Meloni's infrastructure minister in charge of ports, during his brief 2018-2019 stint as interior minister.
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