Rome had originally refused to let the Mare Jonio dock in the latest stand-off between the government and private aid vessels.

Interior Minister Matteo Salvini had on Monday reiterated that Italy’s ports were “closed” to new migrant arrivals, insisting his hardline approach to asylum seekers since last summer has effectively stopped departures from crisis-hit Libya.

“They can be cared for, nourished, clothed, whatever you like, but they won't get permission from me to step foot in Italy,” Salvini said.

A judicial source said a magistrate had ordered that the boat be seized as an investigation is launched into allegations of aiding and abetting human trafficking.

The Mare Jonio, operated by the Mediterranea collective of aid groups, picked up the migrants, including 12 minors, on Monday after their rubber boat started to sink in the central Mediterranean, around 68 kilometres off the coast of Libya.

The vessel took shelter from bad weather off the island of Lampedusa early Tuesday, despite being ordered by Italy to maintain a distance from the coast and turn off its engine, according to its mission head and captain.

“We have people on board who are sick, I have to take them to a place of safety and there are two-metre high waves. I’m not turning off the engine,” Captain Pietro Marrone told the authorities, according to the Italian daily Avvenire.

A 25-year-old with suspected pneumonia was evacuated to Lampedusa for medical attention.

Mediterranea said if the ship hadn’t of rescued the migrants they would’ve drowned or been picked up by the Libyans and “taken back to suffer again the torture and horror from which they were fleeing”.

Salvini, who leads the ruling far-right League, has repeatedly declared Italian ports closed to NGO rescue ships, previously leaving several of them stranded at sea in a bid to force other European countries to take their share of asylum seekers.