The French government has warned that "there will be extremely strong consequences for bilateral relations" with Italy.
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France's government has granted a safe port to the Ocean Viking rescue vessel carrying 234 migrants.
Interior Minister Gérald Darmanin said France would welcome the ship's passengers at the military port in the city of Toulon on Friday.
The Norwegian-flagged vessel -- operated by the NGO SOS Méditerranée -- has been at sea for nearly three weeks.
Italy had refused to allow the migrants to disembark on Italian territory, sparking a dispute with Paris.
Darmanin said the 230 passengers on board the Ocean Viking subsequently would be divided among France, Germany and other European countries.
The French coast guard has already begun a medical examination and four migrants were evacuated from the ship by helicopter for medical reasons.
“All measures will be taken to bring health and medical assistance necessary to the passengers” and to carry out security controls, Darmanin told reporters in Paris following the government's weekly cabinet meeting.
He added that the decision was taken "exceptionally" and that passengers who did not meet the criteria of asylum seekers "would be deported directly".
Some opposition lawmakers have criticised the French government, arguing that by welcoming NGO ships, the country would encourage more migrant smuggling.
Marine Le Pen, the leader of the far-right National Rally, said the move was a "dramatic signal of laxity".
The Ocean Viking had been carrying more than 230 migrants in the Mediterranean Sea for around 20 days.
SOS Méditerranée's director general Sophie Beau had said the situation on board had reached a "critical stage" with the risk of "loss of human life".
After Italy's far-right government refused to grant the ship a safe port, it set sail for the French island of Corsica, hoping to disembark there.
Meloni relents, allows hundreds to disembark
In the meantime, Italy's government backed down on its stance and allowed hundreds of rescued migrants to leave three other NGO vessels, and not just those who were deemed "vulnerable".
Italian Prime Minister Giorgia Meloni caused a diplomatic rift by prematurely thanking the French government on Tuesday for taking in the ship. The French government had made no such pledge publicly at that stage.
Meloni has stated that European countries should share the responsibility for the intake of migrants found in the Mediterranean Sea, particularly if rescue vessels are flying under their country's flag.
But Darmanin slammed Rome's choice as "unacceptable" and "incomprehensible" and has warned that "there will be extremely strong consequences for bilateral relations".
ADVERTISEMENT“France will take measures in the coming hours to tighten the border security with Italy” and adjust bilateral relations accordingly, Darmanin said on Thursday.
"France deeply regrets that Italy did not accept to behave like a responsible European state," he added.
"Managing migratory flows in the Mediterranean is a European problem that touches all of us, calling for a European response".
The French government has now suspended "with immediate effect" the planned arrival of 3,500 refugees from Italy.
The European Commission has unusually taken a stance on a domestic immigration matter and had called for Ocean Viking to "immediately disembark".
ADVERTISEMENTFrench government spokesperson Olivier Véran said that Paris would arrange a meeting with Brussels in the coming days to discuss Italy's position.
Under maritime law, all people found at sea in distress are entitled to access the closest safe port, where they can then apply for asylum.
'Rescue criteria are not discretionary'
France and Italy previously clashed over the Aquarius migrant rescue vessel, which eventually disembarked in Valencia, Spain, in 2018.
"The unbearable situation of the Ocean Viking shows that it is urgent that European states put in place a permanent disembarkation and distribution mechanism [for rescued migrants]," said Sophie Beau, director of SOS Méditerranée.
"The [French government's] solution has a bitter taste because these 234 people have just been through a real ordeal," she told AFP.
ADVERTISEMENT"It's a relief tinged with bitterness, it's really an acknowledgement of the failure of the policies of the European (member) states who have flouted maritime law in an unprecedented way."
The attempt of the Italian government to blackmail the bloc had no legal basis in international law, Fulvio Vassallo Paleologo, former professor of asylum rights and constitutional status of foreigners at the University of Palermo, told Euronews.
"The criteria under which a state rescues migrants are not discretionary -- but are set by international law, like as the Hamburg SAR convention, the EU Frontex regulation as well as the UNCLOS convention. Disembarkment must take place at the nearest safe port and in the shortest time possible," Vassallo Paleologo explained.
"Coastal nations cannot flaunt their obligations by sending migrants to another, far away country that it might take weeks to reach."
"Italy should play by these rules -- but the government doesn't want to do that because of political gains," he said.
ADVERTISEMENTAlso, the Meloni government's demands for more help from other EU member states is not justified by the number of those arriving at Italian ports, according to Vassallo Paleologo.
"The number of migrant arrivals in Italy is not as high as to justify a request for more solidarity from Europe. If you look at the number of asylum applications submitted, Italy has around 50,000 a year while Germany has around 100.000, 150.000 more."