All the migrants will get special 45-day humanitarian permits to stay, and asylum requests will be assessed, Spain has said.
"No human being is "illegal"," added Sy.
The government said in a Saturday statement that France has offered to take in eligible migrants who wish to go to France.
Crews of the NGO boats say Salvini's port closures leaves them without anywhere close by to take the people they rescue, and that the move will prove counterproductive.
Salvini, the leader of Italy's League party, was instrumental in blocking a ship carrying hundreds of rescued migrants from docking this week in his country.
Pope Francis says that the Gospel teaches that it's wrong to leave migrants "at the mercy of the waves", an apparent critique of Italy's new migration policies.
Sea Watch feared that it would end up like the Aquarius, a rescue ship that has been on a dayslong voyage to Spain with 600 migrants aboard after Italy refused it entry.
David Noguera, the head of Doctors Without Borders in Spain, said he was glad Spain welcomed the ship's passengers, who were picked up off the coast of Libya.
Macron had been critical of Italy's refusal to accept the Aquarius migrants but later worked to smooth things over with Italy's Prime Minister, Giuseppe Conte.
Immigration will be a top issue at the European Union leaders' June 28-29 summit.
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While Australia and New Zealand will ring in the festival on Saturday, Singapore and Malaysia are observing it on Friday. King Salman also thanked Allah for having helped Saudi Arabia "remain adherent to Islamic Shariah law".
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Two countries will "work together" to handle the arrival, Spain's deputy prime minister Carmen Calvo said.
As many as 933 people have been rescued in the Western Mediterranean and Straits of Gibraltar over the past 48 hours, the Spanish sea rescue service Salvamento Maritimo said on its twitter account.
"The migrants go to their temporary shelters, and we continue to work with them". I took the decision that they can not come in because it was not our responsibility.
Vessels chartered by an assortment of European NGOs have plied the waters off Libya for three years, rescuing migrants from leaking boats and transporting them to Sicily. The trip to the Spanish port took almost a week. In a Facebook post Saturday, Salvini said Lifeline and the Seefuchs ship of the German group Sea-Eye couldn't dock in Italy. It will be followed by the NGO-run Aquarius and another Italian navy ship the Orione. Spain then stepped in and offered to let it land. He said he is anxious that more European nations will close their ports to migrants who are rescued at sea.
Migrants descended the Italian coast guard vessel Dattilo upon arrival at the eastern port of Valencia, Spain. "The inaction of Europe is criminal", SOS Mediterranee cofounder Sophie Beau told a news conference in Valencia. "I am happy that the journey (for the Aquarius migrants) is over - a journey that was too long - and I am anxious for the situation in the Mediterranean and the closing of European ports". Monica Oltra, left wing vice president of the Valencia regional government, said, "The Mediterranean Sea must not become a mass grave".
Italy had initially insisted that Malta take in the Aquarius rescue ship and the 629 migrants onboard rescued in a series of operations last weekend.
Earlier this week, Malta rejected an Italian demand that it accept the ship, the MV Aquarius, after Italy closed its ports to the vessel, stating that in terms of worldwide law, the migrants should have been taken to the nearest safe harbour.
The migrants will be met by emergency workers, including health officials and psychologists, at the city's marina.
Spanish authorities are interviewing the migrants on a case-by-case basis to see who may qualify for asylum.
On extending the offer Spain's Foreign Minister Josep Borrell said they were doing so "to oblige Europe to forge a common policy to a common problem", the publication said.