According to Italy's Rai state television, 33 bodies including some women and children have been recovered so far after the heavily overloaded boat was toppled as the agitated migrants tried to catch the attention of a military aircraft that was flying over the area, some 104 km south of the Italian island of Lampedusa.
About 200 people have so far been rescued, it added.
The latest accident occurred a week after a shipwreck left more than 300 people dead near the Italian island of Lampedusa.
Earlier reports said some 50 people have died after the boat capsized.
The heavily overloaded boat capsized some 104 km south of Lampedusa, in waters where Malta has search and rescue responsibilities.
A patrol boat of the Armed Forces of Malta (AFM) was first on the scene. Two Italian Navy ships also rushed to the spot after they received an alarm from Maltese authorities.
A total of 150 survivors were placed on a Maltese vessel and another 56, including 10 children, were on an Italian Navy ship, reported ANSA news agency citing rescue sources.
The boat capsized between Malta and Italy
Meanwhile, Maltese Prime Minister Joseph Muscat confirmed 27 deaths in the tragic incident, while saying that 203 people had so far been rescued, BBC reported.
Muscat said the dead included three small children and called on the European Union to bolster search and rescue patrols to prevent further tragedy.