The suspected deaths add to the 29 reported earlier in the week by the Italian coast guard, which said those victims had died of hypothermia during the voyage that began over the weekend in Libya, where most smuggling operations originate.
The UN High Commissioner for Refugees said survivors had reported that four boats had left together, without food or water, and that the boats began taking on water almost immediately.
The nationalities of the survivors and those missing were not immediately given, but a large proportion of those arriving at the moment are fleeing conflicts in Iraq, Syria, Mali and elsewhere.
UNHCR, Save the Children, Amnesty International and other aid groups blasted the new EU-backed rescue patrol as insufficient for the task at hand. The European Union took over Mediterranean patrols after Italy phased out its robust Mare Nostrum operation in November.
But the EU's Triton mission only operates a few miles off Europe's coast - its job is to patrol Europe's borders - whereas Mare Nostrum patrols took Italian rescue ships up close to Libya's coast.
"The Triton operation doesn't have as its principal mandate saving human lives, and thus cannot be the response that is urgently needed," Laurens Jolles, the head of the U.N. agency for southern Europe, said in a statement.
Save The Children called for the EU to urgently meet to restart Mare Nostrum "or another rescue system that has the mandate, the capacity and means to prevent other tragedies."
"Pointing fingers is not going to get us anywhere," Bertaud said in Brussels. "If we want to talk seriously about improving the situation then we also need to talk about financing it adequately."
The commission is currently conducting a feasibility study into whether a border guard system would be worthwhile, with the first discussions expected to begin next month.
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