Libyan Prime Minister Ali Zidan denied the allegations in a press conference Sunday during a visit by Malta Prime Minister Joseph Muscat to discuss the wave of refugees arriving by boat from Libya in Malta and Italy. He pledged an investigation.
UNHCR has expressed concern that Syrians escaping civil war are facing a perilous sea journey to reach safety in Europe.
Two million Syrians have fled to neighboring countries, according to the U.N. refugee agency, and many are continuing the journey through northern Africa to ports where smugglers offer passage to Europe. Hundreds more Syrians have arrived by boat in Italy over the weekend, following a string of recent tragedies.
"Their journey is as life-threatening as the war they escaped," Fleming said.
The latest ship sank in open seas, 65 miles south of Lampedusa in Malta's search-and-rescue area.
Malta's armed forces said there were no plans for divers to be dispatched due to the depth of more than 80 meters (260 feet) unlike another shipwreck eight days earlier in view of Lampedusa where divers have recovered 365 bodies, mostly of Eritreans who fled repression.
Only 155 people survived that tragedy.
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Barry contributed from Milan.