The UN High Commissioner for Refugees says survivors have confirmed the existence of a fourth rubber boat that left Libya on Sunday.
It says that means some 300 people are missing.
The youngest known victim is currently thought to be 12 years old.
The UN, Save the Children and other aid organisations are criticising the new EU border patrol operation as inadequate for saving lives.
The EU’s Triton operation took over Italy’s Mare Nostrum operation last year, but it only patrols close to Europe’s coast. Italy had patrolled the waters up 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 UN agency for southern Europe, said.
The deaths add to the 29 reported earlier in the week by the Italian coast guard, which said the victims had died of hypothermia during the voyage that began on Sunday in Libya.
European Commission spokeswoman Natasha Bertaud said the Triton operation operated by the EU’s Frontex border agency cannot possibly do the job with Frontex’s total annual budget of only €90m.
Mare Nostrum, which has just patrolled the southern Mediterranean, costs Italy €9.5m a month to operate.
She said: “Pointing fingers is not going to get us anywhere. 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.