Sea-Watch on Wednesday accused the Libyan coast guard of threatening to shoot its humanitarian monitoring aircraft over international waters.
The German non-governmental organization posted dramatic footage and audio recordings of the encounter on its social media channels.
On the recording, the coast guard could be heard telling the plane via radio to "get away from Libyan territory, otherwise, we will shoot you," with "missiles."
"Please be informed that you are within European Search And Rescue Area, this is not Libyan territorial waters. This is not Libyan territorial waters, over,'' a member of the Sea-Watch crew flying overhead responded.
Live fire used to sink migrant boat
The confrontation happened on Tuesday while the Sea-Watch plane was on a mission to monitor the interception of migrants in the Mediterranean Sea.
Sea-Watch insists it occurred over international waters under Malta's search and rescue responsibility.
In the footage, it posted of the incident the Libyans could be seen pulling dozens of migrants onto their vessel.
They then shoot live ammunition a the rubber boat setting it on fire and sinking it.
"The people trying to flee are intercepted within EU waters in violation of international law, and the boat is set on fire by gunfire," Sea-Watch said in a statement.
A spokesman for the Libyan coast guard did not immediately answer phone calls and messages from the AP news agency seeking comment.
Mediterranean a deadly route for migrants
It is not the first time European NGOs operating in the Mediterranean reported threats or violent behavior by the Libyan coast guard.
Last year, it released footage of a Libyan coast guard vessel firing at a migrant boat trying to cross to Europe.
According to the International Organization for Migration, there have been nearly 110 000 crossings this year.
At least 62,403 migrants made it to Europe, 45,939 were intercepted at sea and 1,129 disappeared or are feared to have died.
Edited by: Sean Sinico