Many European countries once routinely accepted such migrants. But former front-line countries — most prominently Italy — have adopted a harder line against migrants, saying they have shouldered a disproportionate burden.

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Denied entry to multiple countries, the two rescue ships waited in the Mediterranean for weeks. They zigzagged off the coast of Malta during bad weather. Many passengers got seasick. As European leaders deliberated over what to do, the 32 people aboard the Sea-Watch 3 were stuck in a small cabin with eight beds.

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“If [Europe] cannot tackle this problem with 49 people, how are they going to tackle real problems? It’s ridiculous,” said Ruben Neugebauer, a spokesman for Sea-Watch, one of the German organizations.

On Wednesday, European powers negotiated an end to the standoff that had become emblematic of the continent’s failure to address basic migration issues. Malta agreed to allow the migrants onshore, where they’ll eventually be divided among eight countries: Germany, France, Portugal, Ireland, Romania, Luxembourg, the Netherlands and Italy.

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Another 131 migrants who had been rescued earlier by Malta will also be divvied up, according to a statement from Maltese Prime Minister Joseph Muscat.

Muscat said the NGO boats would be asked to leave Maltese waters as soon as the migrants disembarked. He further warned that the small island country was “going beyond what is required of us” and that “this case shall not act as a precedent.”

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Analysts said Wednesday that it is only a matter of time until Europe faces the same problem again, because it has been unable to draw up an agreement on how to handle new arrivals, even as the overall number of people coming from the Middle East and Africa has plummeted.

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The European Union last year called for a “shared effort” to relocate and resettle — on a voluntary basis — migrants rescued in the bloc’s maritime territory. But nothing has come of that pledge.

“There is no mechanism in place,” said Matteo Villa, a migration researcher at the Italian Institute for International Political Studies. “Europe is just making a mess of a very small problem.”

The fate of the Sea-Watch 3 and a boat from another charity, Sea-Eye, was a consequence of one of the most concrete changes of the past year: the closure of Italian ports to humanitarian rescue vessels.

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Before Matteo Salvini, the Italian interior minister, demanded those closures, boats tended to be welcomed on Sicilian shores. Italy’s coast guard also had a large hand in rescue operations. But Italy has ceded rescue authority in the Mediterranean to the Libyan coast guard, which brings migrants back to African shores rather than taking them to Europe. Meanwhile, the number of charity boats operating in the region has dwindled. Countries across southern Europe have impounded the NGO boats or accused the groups of criminal activity.

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The rate of migration to Europe has declined drastically since the heights of 2015. But the death rate for those attempting the trip across the Central Mediterranean has increased. In 2018, some 23,000 people arrived by sea in Italy, a decline from 120,000 a year earlier. But 1,300 people died making the trip, compared with 2,300 in the year prior.

The decline in arrivals to Italy began before Salvini’s League party came to power, but Salvini has described his closed-door policy as being central to his “Italians First” strategy. During the deliberations over the charity boats, the mayor of Naples said it was “immoral” to keep people drifting at sea and said the city was willing to defy Salvini and open its port to the Sea-Watch. Salvini responded that “left-wing mayors” should “think of their citizens in difficulty, not about [illegal] migrants.”

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The debate over what to do with the 49 migrants had widened a rift in Italy’s governing coalition. After the deal was reached, Salvini voiced displeasure and said that “caving in to pressures and threats from Europe and the NGOs is a sign of weakness that Italians do not deserve.”

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Conditions on the Sea-Watch 3 had deteriorated in the weeks since its Dec. 22 rescue, said Neugebauer, the group’s spokesman. At one point, a migrant tried to jump overboard, thinking he might swim to shore. He quickly realized he had no chance and climbed back onto the boat.

Frank Dörner, a doctor aboard the Sea-Watch 3, said the past couple days had been “very stressful.”

“We’re happy about this solution, but it came by far too late,” Dörner said.

The crew planned to rest and then head back in the direction of the Libyan coast, where it would attempt to conduct more rescues. Once that happened, he said, another standoff could ensue.

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Dörner said: “It may be that we are ending up in a couple days in the same situation.”