Ending a lengthy standoff, Italy allowed 116 rescued migrants on its Gregoretti coastguard ship to disembark on Wednesday after several EU countries agreed to share responsibility for looking after them.

Matteo Salvini, the country’s hardline interior minister, announced he had given his green light earlier in the day after forcing the migrants to remain on the boat docked in Sicily for five days.

Italian prosecutors had opened an investigation into the conditions on the coastguard supply vessel where the migrants had only one toilet between them, Italian media reported.

An EU Commission spokeswoman told AFP earlier Wednesday that France, Germany, Ireland, Luxembourg and Portugal would join the Italian Roman Catholic church in caring for the migrants.

The Commission did not give a breakdown on how the migrants would be shared out between the host countries but the official said most would stay in Italy.

The stand-off was immediately set to repeat itself, with Salvini on Wednesday formally banning the Alan Kurdi – a rescue ship run by German charity Sea-Eye – from entering Italian waters after plucking 40 migrants from waters off Libya.

Salvini has taken a hard line against migrants rescued at sea being brought to Italy, which he says bears an unfair burden.

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