“The ship is German property, with a German flag and a German crew… It's their problem, they must deal with it,” Salvini said on the sidelines of a meeting of G7 interior ministers in Paris.
He said he had personally written to the captain of the Alan Kurdi, operated by the Sea-Eye charity, warning him the ship would “not enter Italian territorial waters.”
The ship on Wednesday rescued 64 people, including women and children, from an inflatable raft after efforts to contact the Libyan coastguard failed.
It is headed for the Italian island of Lampedusa.
Salvini, a leader of the far-right League party, reiterated last month that he would close his country's ports to migrant rescue NGOs operating in the Mediterranean, in a bid to force Europe to take its share of asylum-seekers.
He said Thursday that his stance had been backed by his fellow G7 interior ministers.
“To my great satisfaction, I'm not the only one who has doubts about the NGOs in the Mediterranean,” he said.
“Ask my French, German and British colleagues.”
“Everyone at the table noted it: the NGOs are a problem and they help human traffickers,” he said.
But French Interior Minister Christophe Castaner indicated “disagreements, in particular on the docking of rescue boats in the closest port.”
He added, however, that he had “reaffirmed to the Italian minister France's solidarity with regards to welcoming refugees who might be on these boats.”
Europe has been wrestling with divisions over how to handle the problem since the migration crisis of 2015 when more than one million people arrived on its shores, many of them fleeing conflict in the Middle East.