Earlier this week Somalia's government said about 200 or more Somalis may have died in the tragedy while trying to cross illegally to Europe.
After talking to survivors, the UNHCR says the overall death toll might be much higher.
The UN refugee agency's staff in Greece have met around 41 survivors from Somalia, Ethiopia, Egypt and Sudan, who claim up to 500 passengers were killed during their crossing.
Members of the group say they initially left Libya on a boat with up to 200 people on board, and after sailing for several hours were ordered by smugglers to board a larger ship that was already carrying hundreds of others.
The UNHCR says it was told that during the transfer, the larger boat capsized and sank, killing hundreds of people.
Spokesman William Spindler says the stories told by survivors are a reminder of what is occurring almost daily in the Mediterranean.
"It's not clear how many people were on the boat when it sank. Eyewitness accounts talk about up to 500 people. Women, children, men, we don't know exactly how many were there on that boat and they have now disappeared from the face of the earth. This is another example of what is happening almost on a daily basis in the Mediterranean."
The agency says the survivors - 37 men, three women and a three-year-old child - were rescued by a merchant ship and taken to Greece on April the 16th.
They say they had been among 100 to 200 people who set sail from Libya last week headed for Italy.
After several hours at sea, the traffickers allegedly tried to move them onto a bigger ship that was already packed with migrants.
One of the survivors, Somalian Khalid Omar Dudi, told Al Jazeera about his ordeal.
"There were two boats, a small and a large one. I was in a small one, my friends were in the large one. When we were about to get in the big boat it sank. All my friends died. My cousin was one of them. They were my friends. We started the trip together at home and we travelled together until we got on the boat in Libya."
Egyptian Omar Khalid Ayoun also survived the journey.
"They told us we would take the boat from Libya. First we took a motorboat which took us to a small boat which then took us onto another larger one. We travelled overnight and on the second night the small boat arrived again with food and more passengers, and as they tried to board the boat it capsized. Those who were able to swam. We kept on shouting help, help until a rescue ship arrived. The Italian Red Cross told us to board a boat, that boat brought us to Greece."
This news has emerged 12 months after one of worst disasters in the Mediterranean in recent times, when an estimated 800 migrants drowned off the Libyan coast after the fishing boat they were sailing in collided with a merchant vessel that had been trying to rescue them.
The UNHRC's William Spindler is expecting a fresh surge in the number of people undertaking such perilous journeys.
"We fear that this is the beginning of the good season. The weather is getting better in the Mediterranean and more people will attempt to cross. We have seen already the numbers of people trying increase and we fear that further loss of lives will be inevitable."
The International Organisation for Migration says nearly 180,000 people may have crossed the sea between Europe and Africa so far this year, while hundreds are confirmed dead or missing.
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