Sixty-five people, including one person with disability, two babies and five children were rescued off the coast of Libya, Sea-Watch said on Wednesday.
Eleven women were also on-board a rubber boat found 30 nautical miles off the Libyan coast.
Many of those rescued showed signs of dehydration, exhaustion and sea-sickness, Sea-Watch said. The rubber boat had been spotted earlier by the civilian reconnaissance aircraft Colibri.
Authorities in Malta, Italy, Libya and the Netherlands, which is the flag state of the Sea-Watch 3, have all been informed, the organisation said.
The future for the 65 rescued is still unclear, with a spokesman for the NGO saying the vessel had no clear direction for a port of safety.
AFM declines to comment
Contacted about the incident, a spokeswoman for the Armed Forces of Malta declined to comment, saying it had nothing to add to the Sea-Watch statement.
The Sea-Watch 3 is currently the only dedicated rescue ship in the Mediterranean, which has long been described as the "deadliest strip of sea" worldwide.
While not a single rescue ship was around, the number of boat departures from Libya had increased dramatically. Seventy people died and 240 were forcibly pulled back by the Libyans on behalf of Europe," Philipp Hahn, Sea-Watch 3's head of mission said.
"We are now back to counter this barbarism and to defend European values instead of only repeating them over and over on election posters," he said.
The Sea-Watch was at the centre of controversy after authorities controversially refused to allow the vessel to continue its operations.
The Maltese government had stopped migrant sea rescue ships from entering or leaving local ports early summer. The decision was prompted by investigations against the captain of another Dutch-flagged rescue ship, the MV Lifeline, due to potential issues with the ship's registration.
It had finally set off after 115 days in Malta late last year.
???? BREAKING Upon arrival in the search- and rescue zone #SeaWatch 3 crew just rescued 65 people from a rubber boat in distress, spotted by civil aircraft #Colibri ~30nm off #Libya. The authorities in LY, MTA, IT & NL are informed. #DefendSolidarity pic.twitter.com/oOZs3TEmag— Sea-Watch International (@seawatch_intl) May 15, 2019
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