Migrants from one of four rescue boats that Italy had blocked from docking have been allowed to disembark after a week at sea, the charity that operates the vessel said.
A total of 89 people on board the Rise Above were allowed ashore.
But people remain on three other rescue boats as Rome vows to halt irregular migrants crossing the Mediterranean.
Prime Minister Giorgia Meloni has said she wants to stop people traffickers "deciding who enters Italy".
Her right-wing government has been criticised for denying safe port to the rescue boats.
But Chiara Cardoletti, the UN refugee commissioner's representative in Italy, said that Italy had been on the front line of the migrant crisis for too long and she called on the European Union to find a common strategy.
"We appreciate what Italy has done by allowing boats to enter territorial waters, allowing children, women and people with medical problems to disembark," she told the BBC. "Italy cannot be left alone, the European Union must step forward and find appropriate and faster solutions."
On Monday, three people leapt into the water from the Geo Barents after being refused permission to disembark in the Sicilian port of Catania. They were among about 250 migrants told to remain on two boats in Catania after officials deemed them "healthy".
Mission Lifeline, a German charity that runs the Rise Above, said in a statement that it was "relieved that the rescued people are finally safe on land" at Reggio Calabria on the Italian mainland, a few kilometres from Sicily. Many of the 89 who disembarked were described as minors.
Authorities told Italian media that they had been allowed to leave because they had been picked up in a so-called save and rescue (SAR) incident in the Mediterranean, whereas those on the two boats docked in Sicily were not.
The charity condemned what it called an "undignified political game" that had kept them at sea. The crew of the Rise Above have not yet been able to leave the boat, according to Italian reports.
Mission Lifeline said the Rise Above was by far the smallest of the three vessels in port and its passengers had suffered badly in recent heavy seas.
Migrants set sail in small, overcrowded boats from North Africa, often get into distress and are rescued by charity vessels.
Over the weekend, two boats docked in Sicily, carrying a large group of migrants.
Most were allowed to leave, but 35 men on the Humanity 1 and another 215 on the Geo Barents, which is run by Médecins Sans Frontières (MSF), were told they would have to stay on board.
A fourth boat, Ocean Viking, run by French charity SOS Mediterranée, remains off the coast of Sicily with some 234 migrants aboard. They were picked up from the sea off Libya 17 days ago and have repeatedly demanded access to an Italian port.
SOS Mediterranée said the situation on board Ocean Viking had "reached a critical limit" that required an immediate response.
"We are facing very severe consequences, including risks of loss of lives. Physical and psychological wellbeing of survivors and crew have been exhausted by over two weeks of blockage at sea," said Xavier Lauth, the group's director of operations.
Both SOS Humanity, which runs Humanity 1, and MSF have argued that everyone on board their ships is vulnerable, as they were rescued from the sea.
SOS Humanity is also taking the Italian government to court, alleging that a decree by an Italian minister, allowing the migrants to be kept on the ships, breaks both Italian and international law.
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