An Italian corvette, the Fenice, picked up dozens of migrants aboard a sinking rubber dinghy on Tuesday after the vessel was spotted by a naval helicopter.
Fifty-four were brought to the Italian island of Lampedusa, but according to testimony from survivors, the craft had set off with between 117 and 120 people on board, all of them from sub-Saharan Africa, the IOM said.
Over 30 of the passengers were women but there were no children, the agency said.
More than 2,100 had died in their bid to cross, it said.