Malta's Prime Minsiter Joseph Muscat continued to insist his country is acting according to global law and that it is Italy's duty to take in the migrants, as Italy's coast guard coordinated the rescues off the coast of Libya.
Malta refused, saying it had nothing to do with the rescue mission, which was overseen by Italian coastguard.
Spain's offer is "important news, since it signals a turning point", Di Maio said. "Moreover, the weather conditions are adverse". The ship now carries 629 refugees and migrants rescued from sea off the Libyan coast. The vessel with 123 unaccompanied minors and seven pregnant women on board is stranded in the Mediterranean Sea. The migrants, who were picked up from different boats in Libyan waters, hail from several African countries - including Nigeria, Morocco, Sierra Leone, Algeria and Sudan.
Salvini said Malta should accept the vessel.
Spain's decision to take in the ship was hailed by Italian Interior Minister Matteo Salvini as a "victory" for his government's hardline immigration policy.
Home Affairs Minister Matteo Salvini told Italian media that a second humanitarian ship, the Sea Watch 3, which is now navigating off the Libyan coast, will not be allowed into Italian ports, if and when it is involved in a migrant rescue operation. All three ships would then sail to the Spanish port of Valencia on a voyage expected to take four days.
Doctors Without Borders (MSF), which is operating the Aquarius alongside SOS Mediterranne, urged Rome to drop plans for the lengthy trip to Spain for its migrant passengers.
In the meantime, SOS Mediterranee, another organisation on the Aquarius, tweeted late on Sunday that the ship had "received instructions from the Italian Maritime Rescue Coordination Centre to standby in our current position, which is 35 nautical miles from Italy and 27 nautical miles from Malta".More news: Anthony Bourdain and Kate Spade's deaths are part of a growing problem in the US
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He noted that other European countries are very much involved in current rescue operations in the Mediterranean - including a German aid group now off Libya - but no country is stepping up to actually take in the migrants.
Spain's new Socialist Prime Minister Pedro Sanchez agreed to allow the ship to dock in its eastern port of Valencia.
"It says that the country responsible for operations in that area has primary responsibility for taking them from the ship".
Malta's Prime Minister Joseph Muscat tweeted his thanks to Sanchez "for agreeing to accept the Aquarius after Italy violated global law and caused an impasse".
However, charities questioned why the coast guard boat was being allowed to dock in Italy, while migrants on the Aquarius, who had been at sea for longer, were not.
Salvini, 45, has continued with his anti-refugee rhetoric since taking control of the interior ministry, asking on Friday for North Atlantic Treaty Organisation to defend Italy, which he says is "under attack from the south".