The German non-governmental group Sea-Watch filmed the incident while flying over the Mediterranean in an observation mission.
A non-profit sea rescue group slammed Libya's coast guard on Thursday after it witnessed the Libyan maritime authorities in what it described as chasing a crowded migrant boat and shooting in its direction in an apparent effort to stop it from crossing the Mediterranean Sea to Europe.
Members of the German non-governmental group "Sea-Watch" filmed the incident on Wednesday while flying over the area in an observation mission.
In the footage filmed from the plane, a blue wooden boat with a small engine and at least two dozen people onboard is seen being followed in circles at high speed by the Libyan coast guard.
During the chase, which occurred in international waters under Malta's search and rescue responsibility, men in uniform on the Libyan vessel can be seen firing at least two times towards the boat, with bullets hitting the water close to the boat.
The Libyan coast guard came dangerously close to crashing into the boat several times.
Sea-Watch communicated to the Libyan authorities via radio that they were endangering the lives of the people on the blue vessel and urged them to stop shooting.
The Libyan coast guard replied in broken English that they were trying to rescue the migrants.
"These maneuvers that we have seen yesterday could easily kill persons, like easily. Everyone of us is really wondering how no one has died yesterday," said Felix Weiss, head of airborne operations at Sea-Watch.
"What is new and what is really outrageous in my point of view is as I said that Malta allows (it to happen inside its SAR zone)," he added.
The Sea-Watch aircraft was short on fuel and turned back before the chase ended.
It later received reports the boat had arrived on the Italian island of Lampedusa on Thursday morning.
There was no immediate comment on the incident from Libya, Malta or the authorities on Lampedusa.
The EU trains, equips and supports the Libyan coast guard to intercept people trying to cross the Central Mediterranean to Europe.
Speaking to Euronews in February, the navy chief in charge of the EU operation policing the waters said the European Union should give Libya more autonomy to deal with illegal immigration.
Admiral Fabio Agostini, the head of Operation Irini, said that the best way to stop migrants crossing to Europe was to help prepare the Libyan coast guard for tackling people smuggling.
"I believe that the best way to stop illegal immigration, to contribute to the dismantling of these human smuggling models, is to train the Libyan coast guard, the navy, just because we need to let them be more autonomous in dealing with security issues in their water of responsibility," Agostini said.
At least 723 people are known to have either died or gone missing taking this route on unseaworthy boats so far this year.
Nearly 15,000 men, women and children have been intercepted by the Libyan coast guard and returned to Libyan shores from the start of the year up to June 26, a record number.