The Libyan Coast Guard on Tuesday morning came to the aid of three rubber boats and managed to rescue 300 people.
However, the boat had been carrying 150 migrants, survivors said, with numerous dead vanishing beneath the waves. Its remnants were found off the western city of Khoms, the navy said.
The Libyan Navy said on Wednesday that its Coast Guard had rescued at least 279 migrants off the coast of Libya, but that about 100 more were missing and feared dead.
Since the 2011 fall and killing of longtime dictator Moamer Kadhafi, Libya has become a key launch pad for migrants making desperate bids to reach Europe, often on unseaworthy vessels.
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"The rescued immigrants survived by clinging to the balloon of the boat until the rescue boat arrived from Sabratha city", said the Navy.
"We can proudly say that many among those we resuscitated are now alive", said Maria Rita Agliozzo, a physician from the Order of Malta who, along with a paramedic, was aboard the coast guard rescue ship.
The deaths represent the first major migrant tragedy of 2018 in the Mediterranean Sea.
Mr Di Giacomo said the Libyan coast guard in recent days rescued 250 other migrants from traffickers' boats and recovered the bodies of two women, while survivors said another 10 migrants were missing.
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The vast North African country is home to competing governments and parliaments, with real power held by an array of militias, many of which make money from trafficking and packing hundreds of desperate migrants in unseaworthy boats to make the risky voyage across the Mediterranean.
There was however a sharp drop in arrivals in Italy during in the second half of 2017 following efforts by Rome to discourage migrants from attempting the crossing.
The International Organization of Migration estimates that over 171,300 migrants entered Europe in 2017, compared to a little over 363,500 in 2016.
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