A group of 27 people rescued on Tuesday off Sicily reported that there another 75 people on board their boat, who are therefore believed lost at sea, the agency said in a statement.
Accounts of the shipwreck were gathered by UN workers in Sicily who spoke to survivors recovered by Italy's "Mare Nostrum" ("Our Sea") rescue operation.
"According to the information gathered so far, the shipwreck occurred because the rubber dinghy they were travelling on was in a poor state and was overcrowded," Catania prosecutor Giovanni Salvi was quoted as saying by Italian media.
Salvi has opened an investigation into the shipwreck, news of which came just three days after the bodies of 45 migrants were discovered in the hold of an overcrowded fishing boat, where they appeared to have suffocated to death. The figure is higher than earlier reports that 30 people had died.
The UNHCR said migrants rescued from another boat and brought to safety in Porto Empedocle in Sicily told them two of those on board had died during the crossing, while four others were lost overboard.
It estimated that 500 migrants and refugee seekers have died while attempting the perilous crossing from North Africa to Italy in 2014.
"Despite the huge efforts by the Italian authorities and the constant help offered by private boats, hundreds of innocent migrants and refugees continue to lose their lives at Europe's boundaries," it said.
"The latest tragedies show that the refugees have no other choice but to risk their lives by crossing the Mediterranean to seek refuge from wars and persecution," it added.
The agency called on governments "to provide urgently legal alternatives to the dangerous journeys by sea...guaranteeing to the desperate and those in need of refuge the possibility to seek and find protection and asylum."
Overnight, rescue workers recovered the bodies of 45 migrants who died after being locked by traffickers inside the hull of a fishing boat.
The victims were discovered late Sunday, when the Italian coast guard came to the rescue of a blue wooden boat carrying around 600 migrants from Syria, Eritrea, Somalia and Cameroon.
The number of migrant arrivals has now soared past the record 63,000 set in 2011 during the Arab Spring uprisings, and EU border agency Frontex has warned that calm seas across the summer will encourage many more to attempt the trip.