Cracks emerged Friday in Europe's hard-fought summit deal on migration, as EU President Donald Tusk warned there was no guarantee it would work and France and Austria ruled themselves out of hosting migrant centres.

Cracks emerged Friday in Europe's hard-fought summit deal on migration, as EU President Donald Tusk warned there was no guarantee it would work and France and Austria ruled themselves out of hosting migrant centres.

The agreement, hammered out during marathon overnight talks, also swiftly came under fire from the Medecins Sans Frontieres (MSF) charity, which said it aimed to turn away even the most vulnerable people from Europe's shores.

Underscoring the human dimension of the crisis, the bodies of three babies were recovered and around 100 people were missing after a migrant boat sank off the coast of Libya on Friday.

Italy's new populist government, which has sparked fresh political tensions in Europe by refusing to let a series of migrant rescue ships dock in recent weeks, had initially blocked the conclusions of the Brussels summit.

But after nine hours of bitter negotiations, 28 EU leaders agreed to consider setting up "disembarkation platforms" outside the bloc, most likely in north Africa, in a bid to discourage migrants boarding EU-bound smuggler boats.

The deal also includes plans to set up secure centres on European soil to process new arrivals, to sort refugees in need of protection out from economic migrants who should be sent back.

The central European states of Poland, Hungary, Slovakia and the Czech Republic, which have all taken a tough anti-migrant stance, hailed the agreement as a victory.

But Tusk warned that difficult work lay ahead to make the agreement work in practice. "It is far too early to talk about a success," he told reporters after the end of the summit in Brussels.

"We have managed to reach an agreement in the European Council, but this is in fact the easiest part of the task compared to what awaits us on the ground when we start implementing it."

French President Emmanuel Macron cautioned that Friday's deal "does not solve the crisis we are experiencing" and German Chancellor Angela Merkel acknowledged "we're not at the end of the road yet".

Migrant centres

The plan for "controlled centres" to process migrants who reach the EU was made jointly by France and Italy in a bid to unblock the talks, but Macron immediately ruled out hosting one in his own country.

"France is not a country of first arrival. Because of its situation, France will not open centres of this kind," Macron told a press conference in Brussels.

Macron said the new centres would be reserved for countries on key migrant routes such as Malta, Italy, Spain or Greece.

Austrian Chancellor Sebastian Kurz, who governs in coalition with a far-right anti-immigration party, also refused to host the centres:

"Of course not... we are not a first arrival country, unless people jump from parachutes," said Kurz, who will push the migration issue when his country takes over the EU's rotating six-month presidency in July.

Arrivals have dropped by 96 percent since the peak of Europe's migration crisis in 2015, but the tough stance of Italy's new populist anti-immigration government has thrust the issue back onto the EU agenda.

Italy has turned away a series of migrant boats in recent weeks, and Prime Minister Giuseppe Conte plunged the summit into turmoil by vetoing joint conclusions for the entire agenda until his demands were finally met.

Conte's hardball negotiating tactics infuriated other leaders and an EU source told AFP: "This is a stunt you can only pull off once".

Despite the marathon session, there was no agreement on long-stalled plans to overhaul the so-called Dublin asylum regulations, which say migrants must be dealt with by the first country in which they arrive.

 'Demonising' rescue boats

MSF's emergencies chief Karline Kleijer condemned the deal, saying it aimed "to block people at the doorstep of Europe regardless of how vulnerable they are, or what horrors they are escaping".

And she accused EU leaders of trying to "demonise non-governmental search and rescue operations".

Anti-immigration hardliners accuse NGO rescue boats of exacerbating the situation in the Mediterranean, where migrants try to cross the sea on rickety boats.

Italian interior minister Matteo Salvini on Friday announced that his country's ports would refuse to let NGO rescue ships dock or even refuel for "all summer", saying they "help traffickers, consciously or not".

And Tusk himself had a tough message for the boats.

"We have sent a clear message to all vessels, including those of NGOs, operating in the Mediterranean that they must respect the law and must not obstruct the operation of the Libyan coastguard," Tusk said.

Irish Prime Minister Leo Varadkar agreed, saying that while some NGOs were acting responsibly "there are other NGOs who, even on Twitter, I the last couple of days, are advertising their position – we’re here to pick people up."

In their deal the leaders made an offer to Merkel, who faces a rebellion from within her own coalition government, with moves to stop migrants registered in Italy and other EU countries from moving to Germany.

After allowing more than one million asylum seekers into Germany since 2015, Merkel faces an end-of-month deadline from her own interior minister to curb so-called secondary migration.

And in another win for Merkel, Greece and Spain both agreed to take back migrants from Germany originally registered in those countries.