Rescuers from the island, between Sicily and the North African Italian coastguards also found 25 dead bodies on the same boat as they met it.
The dead refugees were all of young men, who probably died from dehydration and suffocation in the hot summer heat summer heat in the overcrowded hold of the boat.
Italy's secretary of state for immigration Sonia Viale spoke of ‘deep pain’ at seeing ‘once again, so many victims of human traffickers with no scruples.’ Meanwhile Laura Boldrini, from the UN's refugee agency in Italy, called for ‘light to be shed immediately on what happened’.
The victims were apparently the first to board the 45ft-long boat and were packed into the hold "like sardines", according to Italian reports.
The only way they could get onto the deck during the whole three day journey was through an 18 inch wide hatch, in conditions similar to the slave ships which once crossed the Atlantic.
They had asked to be let out of the crowded hold but other refugees didn’t let them, because they were afraid that the deck would get overcrowded and the ship would sink.
The bodies were taken to a morgue on the island which since the beginning of the year has been an escape destination for tens of thousands of refugees from Tunisia, Libya and sub-Saharan Africa. Hundreds of people are thought to have drowned trying to make similar crossings from the coasts of Libya and Tunisia after their boats – often overloaded fishing boats – sank because the engines fail, or some other problem.
Italian magistrates in Sicily, the nearest courts to the island, have started an inquiry into the deaths. Post-mortems will be carried out on the bodies later this week.
"The police will question the other migrants to try to understand exactly what happened on the boat," said prosecutor Renato Di Natale.
Lampedusa, which is only of just 20 square kilometres (7.7 square miles), is Italy's southernmost point and is closer to North Africa than to Italy. It has become the biggest gateway for illegal immigration into the European Union after the arrival of tens of thousands of people from North Africa this year.
The near daily arrivals of refugees from Libya and migrants from Tunisia seen in spring have slowed in recent weeks, with only occasional landings, Agence France Presse reported. Scenes of desperation broadcast earlier this year have hit tourism but many holidaymakers have started returning.