Charlie Yaxley, a spokesman for the United Nations refugee agency, said they estimate "that 150 migrants are potentially missing and died at sea".
UNHCR said that 164 migrants, travelling from Libya to Europe, have died since the beginning of this year, a number fewer than previous years.
"Politicians would have you believe that the deaths of hundreds of people at sea, and the suffering of thousands of refugees and migrants trapped in Libya, are the acceptable price of attempts to control migration", Sam Turner, MSF's head of mission for search and rescue in Libya, said in a statement on Sunday.
In January past year, 64 migrants were killed after an overcrowded rubber dinghy set out from Libya sustained a puncture and sank in the Mediterranean.
The Anti-Illegal Immigration Agency in the capital, Tripoli, said that up to 350 migrants were on board the boats that capsized on Thursday off the coast of the Libyan town of Khoms, around 120 kilometers (75 miles) east of Tripoli.
"The worst Mediterranean tragedy of this year has just occurred", Filippo Grandi, UN high commissioner for refugees, said.
Rescued migrants sit on a coast some 100km east of Tripoli, Libya.
Charlie Yaxley of the UNHCR said he was concerned the survivors could be taken to two detention centres where "there's insufficient food, water, unsanitary conditions".
Thomas Garofalo, director for Libya at the International Rescue Committee, an advocacy group that helps with global humanitarian crises, said migrants "intercepted at sea must not be returned to Libya".
In January, some 117 died or went missing off Libya's coast and around 65 people drowned after their boat sank off the coast of Tunisia in May.
Following the uprising in Libya that killed its dictator Muammar Gaddafi in 2011, migrants from the country have attempted to cross the seas for a better life in European countries.
This is the same detention centre that suffered an airstrike earlier this month that killed at least 50 people and injured 130. However, this has also fuelled trafficking and have led to exploitation by armed groups of migrants, according to The Telegraph.
"An estimated 147 have been rescued and taken back to Al-Khoms in Libya, from where the boat initially departed". More than 200 detainees are still being held at the facility, which is close to where rival Libyan factions have been fighting. The UN has voiced concern for their safety.
The U.N.'s death toll did not include those reported missing at sea Thursday.
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