Updated 9pm

A German NGO said one of its vessels was threatened Saturday by a boat carrying Libyan militants who fired warning shots as it rescued 90 migrants in the Mediterranean.

"We are in shock: we have never been threatened in this way!" Sea-Eye spokesman Gorden Isler told AFP, charging that European Union countries were allowing this "brutal behaviour".

"We were able to get 90 people on board, including two women," Isler said.

After receiving a distress call off the coast of Libya, the crew on the NGO's Alan Kurdi ship located their boat and rescued the migrants.

"While we had already been able to recover 10 people on board, our boat was surrounded by three speedboats with masked and heavily armed people aboard," Isler said.

The militants fired shots into the air and water, where several migrants had fallen in, Sea-Eye said.

The boats with the armed men was flying a Libyan flag.

The NGO said it believed its vessel was not in Libyan waters, adding that it was now headed to the Italian island of Lampedusa with the migrants on board.

Saturday's incident comes a week after 104 people were rescued just off the coast of Libya by the Ocean Viking Ship, run by NGOs SOS Mediterranee and Doctors Without Borders.

The route through Libya to reach Europe is a popular path for migrants from East Africa, the Sahel and the Middle East.

Last month Italy, France, Germany and Malta proposed a system for automatically distributing asylum seekers across the EU to prevent rescue ships from being stranded at sea for weeks. 

But so far only a handful of other nations have backed the plan.