The appeal by the non-governmental organisation follows that of the United Nations refugee agency in Italy that urged the countries involved to "rapidly find solutions to allow migrants and refugees on board the Aquarius to disembark safely and quickly".
"My aim is to guarantee a peaceful life for these youths in Africa and for our children in Italy", he said, using the Twitter hashtag "We are shutting the ports".
Maltese Premier Joseph Muscat also refused to take in the Aquarius ship of the humanitarian group SOS Mediterranee.
However, Mr Salvini does not have authority over the ports and it was not immediately clear if his line would hold. "They manifestly go against global rules and risk creating a unsafe situation for all those involved".
Migrants on April 23 watch the Sicilian coast from the Aquarius vessel as they arrive in Trapani, Italy.
Malta refused, and when Italy instructed the ship to stay at sea, Malta accused Italy of violating worldwide norms.
Earlier, Malta said in a statement that the Aquarius took on the passengers in waters controlled by Libya and where Italian authorities in Rome coordinate search-and-rescue operations.
The agency's special envoy for migrants in the Mediterranean, Vincent Cochetel, underscored that "people are in distress, are running out of provisions and need help quickly".
"Broader issues such as who has responsibility and how these responsibilities can best be shared between states should be looked at later", UNHCR special envoy Vincent Cochetel said.
Doctors Without Borders, which has staff aboard the Aquarius, tweeted a video of some of the women aboard the ship praying on Monday morning, and said they were unaware of the diplomatic drama being waged on land over their fate.
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"Thank you Lord", the women sang.
The League leader defended his decision in a Facebook post, writing: "Malta takes in nobody".
The minister is being seen as making good on "get-tough" anti-immigration electoral promises by banning the boat in a move which has seismic implications for the European Union and global asylum policy.
"From now also Italy begins to say NO to the traffic of human beings, NO to the business of illegal immigration".
Malta, for its part, has consistently refused to take in migrants, citing its small size and limited capacities.
Like Malta, Italy didn't appear to be budging.
The migrants were rescued by Aquarius in six separate night-time operations in the central Mediterranean on Saturday.
"Italy is done with taking orders, this time there is someone saying no".
The MV Aquarius, a search and rescue ship run in partnership between SOS Mediterranee and Medecins Sans Frontieres, has been told by Italian authorities to stand by in its current position, 35 nautical miles from Italy and 27 nautical miles from Malta. Those incidents delayed the migrants' arrival, but they ultimately made it to Italy.
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