The International Organization for Migration (IOM) said the survivors, who were suffering from hypothermia, had reported that there were more than 100 people on board the rubber dinghy when it sank on January 18.
Among those feared missing are 10 women and two children, including a two-month-old baby.
The IOM said most of the migrants were from Cameroon, Gambia, Ivory Coast, Nigeria and Sudan.
The three survivors were rescued by an Italian navy helicopter after air force pilots had spotted a dinghy in distress.
They said they had been in the sea for several hours before help arrived.
Three corpses were seen floating in the water during the operation, and rescuers were unable to locate the dinghy.
Italian President Sergio Mattarella expressed his “deep sorrow for the tragedy that has taken place in the Mediterranean”.
Prime Minister Giuseppe Conte told reporters he was “shocked” by the tragic incident and vowed that Italy would continue to combat human trafficking.
In a seperate incident, around 50 migrants who had left Morocco were reported missing after their dinghy sank in the western Mediterranean.
According to the IOM, 83 people have died so far this year making the perilous journey across the Mediterranean.
