The migrants saved by the Aquarius, run by French NGO SOS Mediterranee, were stuck on the overloaded ship for over 30 hours as Italy and Malta bickered over who should take them before Spain stepped in and offered the port in Valencia as a place for the migrants to land in Europe.
The Aquarius had been instructed by the Maritime Rescue Coordination Center in Rome "to transfer 400 of the 629 refugees and migrants now on board back to Italian Navy ships which will then head to Valencia to disembark", MSF Sea tweeted.
The decision to offer a docking port in the eastern city of Valencia had been a personal and direct move by the country's new prime minister, the Socialist Pedro Sanchez.
But on Tuesday morning, the ship's organizer SOS Mediterranee confirmed that the rescued people will be transferred to Italian ships and sent to Spain.
Malta's ports will not take in the Acquarius vessel with hundreds of migrants and asylum seekers on board, which has been stranded in the Mediterranean after the Italian authorities had refused to accept it.
The Aquarius first headed to Italy, which refused to admit the ship, saying the vessel passed Malta, therefore it was the island nation's responsibility.
They were taken on board its ship Aquarius, which is now between Malta and Sicily. Malta said Italy co-ordinated the rescues and that it has had nothing to do with it. "Maltese Prime Minister Joseph Muscat thanked Sanchez and said Italy had "(broken) global rules and caused a standoff".
Fresh water and food were running low aboard the vessel by Monday afternoon and fresh supplies had to be brought from Italy and Malta.
"Italy has stopped bowing its head and obeying, this time THERE IS SOMEONE WHO SAYS NO. #chiudiamoiporti (#weareclosingtheports)", Salvini wrote on Twitter, as quoted by the Ansa news agency. "This is a European issue". Meanwhile Transport Minister Danilo Toninelli, a member of M5S and the minister in charge of the Italian coast guard, said that "this time everyone has to understand that worldwide law can not mean that Italy should be abandoned". "The priority of both the Italian and Maltese authorities should be ensuring these people receive the care they need".
Mr Salvini says he wants to "stop the death boats".
Italy's new anti-migrant, right-wing interior minister has made good on a campaign pledge to close Italian ports to non-governmental organizations that pick up migrants at sea, which he has likened to taxi services for migrant smugglers. "All a political stunt.at the expense of people in distress?"