The orgnanisation Open Arms says it rescued 106 migrants on Saturday evening around 120 kilometres off the coast of Libya.
The group said it had alerted the Libyan and Maltese coastguards but had received no response.
The rescue took place in darkness and in choppy seas.
The migrants were crammed on an inflatable dinghy with a storm approaching. Open Arms said the operation took place inside the Malta rescue zone.
The NGO's vessel already had 40 other migrants on board who had been rescued earlier after they got into trouble while trying to reach Europe.
For several days last week, Euronews joined the Spanish-led team as they helped rescue those making the perilous Mediterranean crossing, under the eyes of Libyan patrol boats.
Open Arms said that as the mission was taking place they were approached by the Libyan coastguard who falsely claimed they were in its zone.
The group said the officials then observed the rescue from a distance without approaching.
The migrants told Open Arms they had set sail from the port of Shuara on the Libyan coast on February 12.
After seeking permission from the Italian authorities all 146 passengers were disembarked in Sicily.