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”.
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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.
Italy is one of the main entry points into Europe. Since the start of the year, 85,000 migrants have arrived on boats, according to the UN.
From North Africa, migrants embark on small, crowded boats, frequently experience distress, and are rescued by charity ships.
Two boats that were carrying a large number of migrants arrived in Sicily over the weekend.
The majority were given permission to leave, but 35 men on the MSF-operated Humanity 1 and another 215 on the Geo Barents were informed that they would need to remain on board.
With about 234 migrants on board, a fourth boat, Ocean Viking, operated by the French humanitarian organization SOS Mediterranée, is still off the coast of Sicily. They have repeatedly demanded access to an Italian port since being rescued from the sea off the coast of Libya 17 days ago.
The situation on board Ocean Viking had “reached a critical limit,” according to SOS Mediterranée, necessitating an immediate response.
“We risk suffering very serious consequences, including possible life losses. After more than two weeks of being blocked at sea, the survivors’ and crew’s physical and psychological well-being has been exhausted “said Xavier Lauth, the organization’s operations director.
Both MSF and SOS Humanity, which operates Humanity 1, have argued that because their ships were rescued from the sea, everyone on board is vulnerable.
Additionally, SOS Humanity has filed a lawsuit against the Italian government, claiming that a minister’s order allowing the migrants to be kept on the ships violates both Italian and international law.