Mediterranea's Italian-flagged 'Alex' sailboat with 41 migrants on board was on Saturday joined by German charity Sea-Eye's vessel Alan Kurdi, carrying 65 shipwrecked migrants rescued off Libya.
Italian populist Salvini last month issued a decree that would bring fines of up to 50,000 euros ($57,000) for the captain, owner and operator of a vessel “entering Italian territorial waters without authorisation”.
“We are waiting in international waters off the island of Lampedusa,” Sea-Eye tweeted from the Alan Kurdi.
“The Guardia di Finanza came by in person to deliver Salvini's decree: The port is closed,” it said, referring to customs officers.
German Interior Minister Horst Seehofer tweeted that Germany was ready to take in some of those rescued “as part of a European-solidarity solution.”
Sea-Eye said the 64 men and one woman were rescued from an overloaded blue dinghy lacking sufficient drinking water, and there was no satellite phone or navigation aid on board.
Salvini accuses NGO rescue vessels of helping smugglers and said the other vessel, Alex, should sail for the Maltese capital Valetta after 13 “vulnerable” people were on Friday taken to Lampedusa, leaving 41 on board.
Valletta has also told the Alex to go to Maltese waters to disembark the migrants, but Mediterranea says the journey would be too arduous.
Photographs showed dozens of migrants and asylum-seekers seeking shelter from the sun under survival blankets on the narrow deck of the 18-metre (59-foot) sailboat.
“In these conditions it is impossible to face 15 hours of sailing. We are waiting for Italian or Maltese naval arrangements to take these people on board,” Mediterranea's Alessandra Sciurba said on Twitter.
She said that while Italy had taken families and pregnant women from the small vessel, “all non-accompanied minors remain on board, including an 11-year-old.”
Mediterranea consists mainly of left-wing activists, the avowed enemy of Salvini, who has seen his popularity and that of his Lega party rise thanks to his tough stance against migrant rescue ships.
A poll published in Italy's Corriere della Sera newspaper on Saturday said 59 percent of Italians approved of Salvini's closing ports NGO vessels.
Italian authorities on Lampedusa last week seized a vessel belonging to German aid group Sea-Watch and arrested its captain, Carola Rackete, for unauthorised entry to port with dozens of rescued migrants on board.
An Italian judge this week ordered her freed as she had been acting to save lives, a decision which also sparked Salvini's ire.
Two other investigations, on charges of helping people smugglers and resisting the authorities are still underway after she forced her way past Italian customs vessels.
Salvini on Saturday repeated his call for reform of the European Union's Dublin rules, which stipulate that asylum requests be handled by the country where they first arrive.
“It doesn't seem that the majority of European countries want to do it,” said Salvini, vowing to change rules he says place an unfair burden on Italy.
“We want to overcome rules that don't work,” he told journalists in Milan.
Despite Salvini's apparent firmness about closing Italian ports to migrants, dozens of migrants and asylum-seekers continue to arrive in Italy by other means, some rescued by Italian authorities.
Interior ministry figures showed 191 had arrived by sea over the last week.
A makeshift vessel carrying 86 people across the Mediterranean from Libya sank off the Tunisian coast on Wednesday, with all but three of them missing or dead.
The Italian judge in last week's Sea-Watch case ruled that neither Libya nor Tunisia were safe countries for migrants.
Libya, which has been wracked by chaos since the 2011 uprising that killed veteran dictator Moamer Kadhafi, has long been a major transit route for migrants, especially from sub-Saharan Africa, desperate to reach Europe.
On Tuesday night, 53 migrants were killed in an air strike on their detention centre in a Tripoli suburb.