Supplies on the ship are beginning to run low and a number of people are in need of medical treatment, including 15 with serious chemical burns and several others suffering from hypothermia, according to Doctors Without Borders (MSF), which operates the rescue ship Aquarius alongside SOS Méditerranée.
The migrants had been rescued from flimsy smugglers' boats in the Mediterranean during a series of operations Saturday by Italian naval ships, cargo vessels and the Aquarius itself.
Mr Salvini also took aim at other European countries that were involved in rescue operations in the Mediterranean but did not actually take in any migrants.
"International maritime law does not provide for specific obligations which would determine in all cases which state is responsible to allow disembarkation on its territory", the United Nations refugee agency (UNHCR) says.
Migrants on April 23 watch the Sicilian coast from the Aquarius vessel as they arrive in Trapani, Italy.
But they need the cooperation of the Italian coastguard.
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The standoff marked the first inevitable clash over migrant policy with League leader Salvini, who is now running Italy's Interior Ministry.
"If anyone thinks I won't move a muscle while we have another summer of landings, landings and more landings, well that's not what I'm going to do", Salvini told reporters. SOS Mediterranee spokesman Mathilde Auvillain said the ship was "heading north following instructions received after the rescues and transfers" on Saturday night.
Matteo Salvini, Italy's Interior Minister and Northern League party leader chose to refuse docking to "Aquarius" and redirect the vessel to the Island of Malta, apparently in line with his election promises.
Spain's Prime Minister Pedro Sanchez, who took office just over a week ago, has given instructions for the boat to be admitted to the eastern port of Valencia, his office said in a statement.
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The mayors of Naples and Reggio Calabria - two coastal cities in mainland Italy - also said they would allow the ship to dock.
Increasing safe returns for migrants to their countries after fair and efficient procedures is a reasonable policy objective.
Charity boats operating off the Libyan coast have played an increasingly important role in rescuing migrants who are often put to sea in flimsy inflatable boats not designed for the open sea.
The Commission says the legal circumstances dictating who should accept the migrants is "anything but clear", however Brussels says both parties are obliged to cooperate to resolve the matter. While he agreed that there should be a more fair distribution of migrants in the European Union, he said Salvini was "making a point at the cost of people in distress".
The Maltese prime minister also expressed concern over the Italian authorities' directions given to the Acquarius vessel, adding that such policies contradicted worldwide norms, and might lead to risky developments.
The French organisation said that 123 unaccompanied minors, 11 small children and seven pregnant women are among those brought on board. Those incidents delayed the migrants' arrival, but they ultimately made it to Italy.
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The news was met with cheers in Gaza, where at least 120 Palestinians were killed by Israeli forces during recent protests. There was no initial reaction from the Israeli FA or from Israeli politicians.