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.
Charity ship Ocean Viking rescued 109 migrants off the coast of Libya on Tuesday, Doctors Without Borders (MSF) has announced.
The migrants were picked up in two separate operations, MSF, who runs the ship alongside SOS Mediterranee, said on Twitter.
"(We) have just rescued 48 people from a wooden boat in distress, 53 nautical miles from the coast of Libya. Women, very young children and a newborn are among the survivors now safely onboard," it first said, adding that it was "heading to investigate another possible case."
It announced three hours later that it had carried out a second rescue operation.
"Many of the 61 survivors are being treated by MSF medics for fuel inhalation. This brings the total number of rescued people onboard Ocean Viking to 109," it added.
The rescue operations came just hours after the ship's return to the Mediterranean.
It disembarked 82 migrants on the Italian island of Lampedusa on Saturday, after the country's new coalition government granted them access, six days after they were first picked up.
The previous government, which included the far-right League party of Matteo Salvini, had banned rescue ships from entering its territorial waters, threatening prison terms for the captains and fines of up to €50,000.
The European Union has struggled to find a common policy to tackle the migration issue with rescue operations usually followed by wrangling between member states to determine where the migrants would be disembarked.
Germany's Interior Minister Horst Seehofer said on Friday in an interview with the Suddeutsche Zeitung that the country was prepared to welcome 25% of the migrants disembarked in Italy.
According to the European Council, 476,097 lives have been saved in rescue operations in the Mediterranean Sea since 2015. It estimates that more than 11,500 people are dead or missing.