The migrants will “disembark in international waters”, Prime Minister Joseph Muscat tweeted from the UN General Assembly in New York.
They will be taken to Malta and “immediately redistributed” to the four countries, a government spokesman said, amid a brewing crisis over their fate.
“The operation will take place as soon as logistically possible,” the spokesman said of the migrants rescued off the coast of Libya by the ship run by charity SOS Mediterranee.
The Aquarius passengers include 17 women and 18 minors and are exhausted and in psychological distress, the NGO said.
France will take 18 while Germany and Spain will each welcome 15, a French government source told AFP.
Portugal will take 10.
The NGO had said that the Aquarius – the last civilian rescue boat in the Mediterranean – was heading for Marseille, “its only option” after Italy’s populist government refused access to its ports.
But the French government had signalled that it was reluctant to welcome the vessel, saying it should dock at the nearest safe port to its current location near conflict-torn Libya.
Malta’s announcement came after talks with the French government, Muscat said.
The Aquarius will then head to Marseille “to rectify its stateless position”, the government said, after Panama announced on Saturday it would revoke the boat’s flag registration following an Italian complaint.
A similar crisis was defused in August when five different countries took in migrants the Aquarius had picked up during the treacherous Mediterranean crossing.
The Aquarius was at the heart of a blazing diplomatic row in June when it became stranded with more than 600 migrants onboard following a refusal by Italy and Malta to take it in.
It has since been repeatedly turned away by Italy and been forced to stop in Malta and Spain after missions in recent months.
Under a previous deal reached in August, 141 migrants onboard the Aquarius were distributed among France, Germany, Luxembourg, Portugal, and Spain.
Italy’s far-right Interior Minister Matteo Salvini has vowed to block the Aquarius permanently from his country’s ports, accusing it of offering a “taxi service” for migrants from Libya to Europe.
His government says that Italy has had enough of migrants arriving by boat, with more than 700,000 landing on its shores since 2013.
The numbers have dropped sharply since their peak in 2015, but the UN’s refugee agency, the UNHCR, has warned that the death rate during Mediterranean crossings has soared.
At least 1,730 people have died trying to make the treacherous crossing in flimsy boats this year, according to the International Organisation for Migration.
The Aquarius has become a symbol of bitter divisions in Europe over how to share responsibility for the hundreds of thousands of people arriving by boat since 2015.
French President Emmanuel Macron has clashed with the Italian government over its blocking of rescue ships, accusing it of “cynicism and irresponsibility”.
He faced criticism at home for not offering safe haven to the Aquarius after it first became stranded in June, although France eventually offered asylum to about 80 of the rescued migrants.
Yesterday his aide blasted Rome for blocking a new permanent solution to manage the docking and distribution of migrants rescued by charity boats.
“It’s not moving forward because those who criticise the lack of French or European solidarity, starting with Italy, don’t want a permanent, durable mechanism,” the aide said.
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