Migrants onboard the Open Arms rescue ship disembarked the vessel at the Italian port of Lampedusa late last night after spending 19 days stranded at sea.
It comes after an Italian prosecutor ordered the seizure of the ship.
Almost 100 migrants, rescued off the coast of Libya, had been on the ship — and Tuesday saw 15 of them jump off the boat in a desperate bid to escape deteriorating conditions.
The Spanish government said it would send a navy ship to the Italian island of Lampedusa to escort the Open Arms rescue ship back to Spain.
"The Audaz will depart this afternoon at 5 pm and will sail for three days to Lampedusa, where it will take charge of the people hosted by the Open Arms and escort the boat ... to the port of Palma in Mallorca," the Socialist government said in a statement Tuesday.
Overnight Monday, eight migrants on board the rescue ship required urgent medical attention and were evacuated from the Spanish vessel to the Italian port of Lampedusa.
One other migrant accompanying them also disembarked.
How did we get here?
Italy has taken a hard line on migrant entry, of the opinion it has borne too much responsibility for coping with African migration to Europe.
The migrants, most of whom are African, had hoped for days to disembark on the southern Italian island of Lampedusa.
However, Salvini ordered his officials not to let them do so, although he made a partial concession on Saturday by allowing 27 minors to leave the boat.
Salvini's political rival, Transport Minister Danilo Toninelli, who controls the Coast Guard but not port access, had offered to take the migrants on a Coast Guard vessel to Spain.
However, he set the condition that Madrid removes the Open Arms' Spanish flag, de-registering it.
Without this, the ship would have difficulty running future rescue missions, its insurance would be invalid and it could be intercepted at any time by a navy or coast guard force.
Open Arms said this was not an option. "They want to take the flag away from us. The price is very high," Spain's El Mundo newspaper cited Open Arms' director and founder, Oscar Camps, as saying on Tuesday.
UN Refugee Agency and Open Arms founder call for action
"Disputes ... anxiety attacks ... panic ... what else do we need? For people to die?" asked Camps. "Those who didn't die in the sea need to die here on board Open Arms? Is this what we need? I hope the Italian courts resolve the situation.”
The UN Refugee Agency on Tuesday called for a halt to using migrants aboard the rescue ship as though they were hostages and for an end to what it said was those using their desperate situation for political gain.
"It's a very simple issue and it's that they can land," a spokesperson for the agency said, adding that six European Union (EU) countries have offered to receive the 100 migrants once they disembark.