The first steps to relocate migrants who were kept at sea by Italy for nearly three weeks has begun as a new crisis loomed with more than 350 rescued people still on board another rescue ship in high seas.

The Ocean Viking, operated by the Doctors without Borders and SOS Mediterranee aid groups, has been on standby since it completed the rescue of 356 men, women and children in the central Mediterranean nine days ago.

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The ship is in international waters, about 32 nautical miles from European shores between Malta and the Italian island of Linosa. Both countries have refused it permission to unload the migrants.

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The situation on board remains under control, SOS Mediteranee head of mission Nick Romaniuk said on Wednesday. "But we cannot resist forever," he added.

The group said on Twitter that people are sleeping on the floor, and there are a limited number of showers and limited water capacity.

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"These people have suffered enormously, most of them have gone through detention centres in Libya," SOS Mediteranee said. "They need to disembark as soon as possible."

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France has confirmed that it will take some of the migrants, repeating the model of an agreement reached earlier this week by some European Union members with a separate group of migrants rescued in early August by Open Arms, a vessel run by a Spanish aid group.

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European countries have been at odds over how to handle the steady flow of economic migrants and asylum seekers who take the perilous journey across the Mediterranean, often putting their lives in the hands of trafficking gangs.

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Despite the number of sea arrivals having dropped sharply from 2015, Italy's hardline interior minister has become a symbol for Europeans who reject migration. Matteo Salvini has closed Italy's ports to the boats of humanitarian rescue groups and accused them of colluding with human traffickers.

His handling of the migrant crisis has boosted his popularity at home, and exposed the EU's shortcomings in offering a unified approach to the challenge posed by sea arrivals of migrants.

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On Wednesday, Doctors without Borders called on Europe to urgently find a solution to the repeated stand-offs barring humanitarian rescue ships carrying migrants from the nearest safe ports.

Maribel Tellado, campaign director for the Spanish chapter of Amnesty International, said the crisis was "a result of the fracas of European migratory policies".

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An Italian prosecutor is probing possible kidnapping and other charges resulting from the refusal of Mr Salvini to allow a large group of migrants from Africa and the Middle East to get off the Open Arms, as well as the failure of officials to assign a safe port and provide hygienic conditions and health care once the boat was in Italian waters.

The aid group had repeatedly warned of an emergency situation on board, which resulted in the evacuation of nearly 70 of the 163 migrants it had rescued off Libya in early August.

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After 19 days at sea, most of them a short distance from the shores of Lampedusa, Sicilian prosecutor Luigi Patronaggio ordered the seizure of the ship late on Tuesday, as well as the immediate evacuation of its 83 remaining passengers.

Mr Salvini had refused to open the port of Italy's southernmost island even after Spain, Portugal, Germany, France and Luxembourg agreed to take the migrants.

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Romania had also offered to take some of them, but its help was no longer needed, European Commission spokeswoman Natasha Bertaud said.

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The EU's executive branch said Brussels would supervise the relocation of the 83, working together with Italian authorities.

Ms Bertaud also said the EU's border and asylum agencies will pre-screen them to begin establishing whether they are eligible for international protection.