Italian police escorted a charity ship into the port of Lampedusa on Tuesday March 19th, after it rescued 49 Africans in the Mediterranean, Reuters has reported.
Meanwhile, Interior Minister Matteo Salvini has called for the crew to be arrested.
Citing a judicial source, Reuters said that a magistrate had ordered that the boat, the Mare Jonio, be seized as an investigation is launched into allegations of aiding and abetting human trafficking.
The Italian charity vessel picked up the migrants, including 12 minors, on Monday after their rubber boat started to sink in the central Mediterranean, some 42 miles (68 km) off the coast of Libya.
The humanitarian ship immediately set sail for the nearby Italian island of Lampedusa, defying Salvini, the leader of the hard-right League party who has ordered the closure of all ports to boats carrying rescued migrants.
After initially being prevented from docking, the Mare Jonio was unexpectedly accompanied into port by police at nightfall as a storm approached.
The judicial source said the migrants would be allowed to disembark, while the boat would be impounded with its crew likely to face questioning.
On his Twitter account Salvini wrote: "Excellent, we now have in Italy a government that defends the borders and enforces the law, especially against human traffickers. Those who make mistakes pay the price," he added.
Repeatedly, the government has accused charity rescue boats of being complicit with people smugglers, who charge large sums to help migrants get to Europe. However, the NGOs involved reject this accusation.