Updated at 11am

President Sergio Mattarella has made a rare intervention in Italian politics to end a dispute within the ruling coalition over a migrant boat, angering right-wing Interior Minister Matteo Salvini.

Mattarella contacted Prime Minister Giuseppe Conte late on Thursday to express his concern about the plight of 67 migrants rescued at sea and brought to a Sicilian port. Salvini had refused to allow them to disembark.

The ship had been brought to the port of Trapani with the approval of Transport Minister Danilo Toninelli, but Salvini ordered that no one should leave the boat until alleged violent conduct by some of the migrants had been investigated.

Toninelli is from the anti-establishment 5-Star Movement, while Salvini heads its coalition partner, the right-wing, anti-immigrant League.

After receiving Mattarella's phone call, Conte, an academic who is close to 5-Star but not a member of either party, ordered the migrants be allowed off the ship. Salvini said he had learned of the president's move with "regret and amazement".

Relations have often been tense between Salvini and Mattarella, who has a largely ceremonial role and intervenes in politics only in exceptional circumstances.

After inconclusive elections in March, Mattarella rejected Salvini's request to be named prime minister and this week he refused to defend the League after a court ordered that its funds be sequestered over a corruption case.

Salvini tweeted on Friday that he would not let the case of the migrant boat lie, using capital letters to say someone "has to pay" if the migrants had been violent.

Hours before Mattarella stepped into the case, Salvini had vowed not to authorise them to disembark, saying: "If someone does it in my place, he will assume the judicial, moral and political responsibility for it."

The League and 5-Star, who were pre-election rivals, formed a coalition on June 1, pledging to crackdown on migration even though arrivals from Libya, where people smugglers operate with impunity, are down more than 85 percent this year.

Salvini has led a high-profile campaign to shut humanitarian rescue ships out of Italy's ports, a move supported by 5-Star. But Salvini's tough immigration stance, which dominates the media agenda, has recently appeared to rankle his allies.

5-Star leader Luigi Di Maio said on Thursday it was impossible to prevent the Diciotti docking because it carried an Italian flag, and on Friday he backed Mattarella's decision to intervene, saying "we have to respect the president."

The supply vessel picked up the migrants on Monday and later asked the Italian coast guard to take them off its hands, citing concern about their aggressive reaction when it seemed they might be returned to Libya.

Salvini said either someone should be charged for threatening the crew of the Italian supply ship, or the captain lied about tensions on board to convince the coast guard to intervene, in which case his company "must pay", he said.

"I don't want to be fooled with. Until there's clarity about what happened, I won't authorise anyone to disembark the Diciotti," Salvini said.