The migrants were picked up from eight rubber dinghies, one large boat and two punts during 11 rescue operations.
Over 80 people have been rescued from the capsized boat; the number of drowned is yet unknown.
The medical relief charity accused European governments of failing to come up with a solution to the crisis and to provide alternatives to the deadly crossings.
Following the plan by the EU and Turkey to turn back refugees, many are looking for alternative ways to reach Europe. Syria
One boy died in the first casualty of the boat crossings in 2016.
As the year draws to an end, Europe's commitment to its humanitarian values is haunted by an unprecedented number of refugees drowning in the Mediterranean Sea.