About 100 migrants are missing at sea, feared dead after their boat capsized off the coast of Libya, the North African country's coast guard said.

Spokesman Ayoub Gassim said the coast guard rescued 14 migrants but he could not provide definitive numbers for the migrants who were on board or their nationalities.

The boat capsized east of the capital Tripoli and the 14 were rescued on Friday, he said.

It was unclear when they embarked on the perilous trip for Europe or from where they had set off.

Libya has emerged as a major transit point to Europe for those fleeing poverty and civil war elsewhere in Africa and the Middle East.

Traffickers have exploited Libya's chaos following the 2011 uprising that toppled and later killed longtime dictator Muammar Gaddafi.

The incident happened just a day after a group of 234 migrants landed in Malta on the charity boat Lifeline on Wednesday evening after being stranded at sea for six days, with both Italy and Malta saying its captain violated international law and refusing to allow it entry to its port.

Earlier, they had also had denied entry to another charity ship, the Aquarius, which was then taken on by Spain. Malta has since effectively decided to close off its ports to most NGO vessels.

In the early hours of Friday, European leaders reached a deal on migration after tense and lengthy talks. Differences, however, remained. EU leaders agreed to share out refugees arriving in the bloc on a voluntary basis and create "controlled centres" inside the European Union to process asylum requests.

They also agreed to share responsibility for migrants rescued at sea.

Fewer than 45,000 migrants have made it to the European Union this year, according to United Nations data, a sharp drop from the wave of 2015 when many thousands were entering on a daily basis.

But the political tremors are still being felt across Europe, with populist, anti-immigrant parties on the rise in many countries.

Ex-communist easterners led by Poland and Hungary are still refusing to accept a share of the new arrivals to alleviate the burden on countries like Italy and Greece.

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