Migrants aboard the charity rescue ship Aquarius will be transferred to a patrol boat in international waters and taken to Malta, before being sent to four other European Union states, the Maltese government said on Tuesday.
"Malta and France again step up to solve migrant impasse," Maltese Prime Minister Joseph Muscat said on Twitter. "With (French President) Emmanuel Macron and other leaders we want to show multilateral approach possible."
The 58 migrants on the Aquarius "will be transferred onto a Malta armed forces asset in international waters" and brought to Malta before being sent onto four EU states, Muscat's spokesman Kurt Farrugia tweeted.
Portugal is set to take 10 migrants from the Aquarius 2 ship as part of a deal with France and Spain, according to a deal announced early Tuesday evening.
In a statement, Portugal's interior ministry said the move was humanitarian and a "response of solidarity to the flow of migrants seeking to reach Europe across the Mediterranean".
But they added that they would continue to support a "stable and permanent" solution to Europe's migration crisis.
It is not yet known exactly what will happen to the remaining migrants.
Earlier on Tuesday, France said they were not ready to allow Aquarius 2 to dock in the southern port city of Marseille.
French Finance Minister Bruno Le Maire said on BFM TV earlier in the day the country is not ready to accept its 58 migrant passengers due to European rules.
"For the moment it's 'no'," Le Maire said, adding that under European rule, ships are supposed to dock at the nearest ports and Marseille is not the closest port.
Aquarius 2 is the one remaining charity rescue vessel still operating in the Central Mediterranean area, picking up migrants who are in many cases trying to get to Europe from Libya.
SOS Mediterranee and Medecins Sans Frontières, the charity groups involved in running the rescue ship, suffered a major blow on Monday when in addition to the recent barring of their boat at Italian ports, Panamanian authorities revoked the vessel's registration.
Aloys Vimard, MSF coordinator aboard Aquarius said: "We are really focused on maritime operations, we have not received official information about the ship, but it is clear that this is related to the political pressure and the Italian government's economic development on Panama. But if that's confirmed, it's terrible, because it will take time for the Aquarius to get a new flag, and in the meantime, lives will be lost at sea."
According to SOS Mediterranee, a maritime-humanitarian organisation known for their rescue missions in the Mediterranean, this is the most deadly sea route in the world and more than 1,250 migrants have drowned at sea since the beginning of 2018.