The Libyan navy has admitted to a confrontation with the refugee rescue boat, according to a navy spokesman, after the crew reportedly refused to identify themselves. However, the navy denied that they boarded the boat on Thursday (25 August), or firing directly at the boat, chartered by the charity Médecins Sans Frontières (MSF).

"A Libyan coastguard patrol was about 25 miles offshore, she observed an unidentified vessel to which the order was given to stop, but [the vessel] did not comply," Brig Ayoub Qassim, a spokesman for the Libyan Navy, said, according to Radio France International.

Qassim added: "We fired five warning shots. We did not storm the boat, we are categorical [about that]. And the patrol then returned to the coast. We informed Operation Sophia" (the EU naval operation based off the coast of Libya) "of this incident and we have opened an investigation. We are the Libyan coastguard and the boat should stop and identify themselves."

The account differs from the one given by MSF, who claim that the Libyan ship set off a volley of bullets, which were aimed directly at the Bourbon Argos.

Thommaso Fabbri, MSF's head of mission said there were "dozens of bullets" that hit the control room and their crew had to hide for safety.

The aid group also say that the armed men came aboard the boat for at least 50 minutes to search the vessel, which had no refugees on board at the time.

The MSF logo is clearly displayed on the side of the ship and its identity is on the automatic identification system (AIS) which every ship and naval authority has access to.

The Bourbon Argos has been operation in the seas off the coast of Libya for over a year, saving the lives of many thousands of asylum seekers fleeing Libya and attempting to reach Italy. In June 2015, the rescue ship saved 1,057 migrants, who were stranded in the Mediterranean Sea using dilapidated boats with little hopes of getting to land in Europe.

Libyan forces state that they were not warned of the rescue operation conducted by MSF on that day.