International Organization for Migration says over 1,800 people have died attempting the North Africa to Europe crossing so far this year.
Officials says some 30 people are believed to be missing, and the body of a boy and a woman were recovered from one of the vessels.
Both flimsy boats are believed to have set off from Sfax in Tunisia on Thursday.
On Sunday rescue teams also used helicopters to rescue 20 migrants found clinging desperately to jagged rocks off Lampedusa’s coastline.
The migrants had been there since late Friday, after their boat was tossed onto the rocks by strong winds.
The central Mediterranean crossing from North Africa to Europe is the world’s deadliest, with over 1,800 people having died attempting it so far this year.
