Among the 83 people rescued were three babies who were revived by medical teams.
"A tragic day in the Mediterranean. The Aquarius was mobilised for a rescue of a deflated boat," the rescue charity SOS Mediterranean said on Twitter. "People were already in the water, 83 people saved and safely on board. Two women could not be revived, leaving two children orphaned."
Doctors Without Borders (MSF), who also helped in the rescue operation, said "many people are missing and presumed drowned, including children."
Italian coast guards on Saturday said a total of 800 people were rescued in five separate operations.
According to the Italian home office, around 2,730 migrants from Libya have landed on the Italian coast since the start of the year.
The numbers have dropped significantly since Italy forged a controversial Brussels-backed deal last summer with forces in Libya to block migrants from setting out for Europe.