The NGO faces a fine of up to €901,000.
The migrants were picked up in two separate operations off the coast of Libya, MSF, who runs the ship alongside SOS Mediterranee, said on Twitter.
Italy's fire brigade rescued a cow stranded near the coast in Stintino, Italy.
Officials told Reuters most of the victims were women and children who could not swim.
In this immersive report, you can accompany the 2nd Battalion of the Military Emergencies Unit during its annual severe winter storms rescue manoeuvres in the Sierra Nevada mountains in southern Spain.
Miners enter rescue tunnel to find missing Spanish 2-year-old believed to be trapped in well
Engineers say they have been delayed in digging a tunnel across to find the two-year-old boy.
Rescue workers are desperately hoping that Julen Rossello will still be alive by the time they reach him.
A baby boy has been found alive on Tuesday (January 1) after 35 hours spent in freezing cold in the rubble of a Russian apartment block that partially collapsed in an explosion.
High pressure pumps and divers from the Indian Navy were brought to Ksan in northeastern India on Saturday (December 29) to aid rescue operations for 15 coal miners trapped underground since December 13
Rescued migrants en route to Spain have been keeping their Christmas spirits up amid likely difficult conditions at sea.