An unidentified armed group shot at and raided a European rescue boat off the coast of Libya, it has emerged, raising questions over the viability of refugee rescue operations in the southern Mediterranean.

On 17 August an unidentified speedboat fired at the Bourbon Argos, a rescue boat chartered by Médecins Sans Frontières, hitting the window of the bridge shortly after 9.30am. The MSF team managed to retreat to the ship’s safe room before the armed men boarded the Argos. Unable to reach the crew, the intruders then left after an estimated 50 minutes without taking anyone or anything, and without giving any concrete indication of why they had come.

However, prior to their arrival, the attackers appeared to be shooting to kill, said Stefano Argenziano, operations coordinator for the MSF mission. “[We speculate that] They were not warning shots,” he said. “There were a number of bullets shot at us from a distance – with an intention, we believe, to harm and potentially kill. We received at least 13 bullets, hitting different parts of the bridge. People who were on the bridge, the command-and-control part of the ship, could have been killed or seriously harmed.”

In a statement, MSF said: “MSF believes that the intruders aimed to physically harm the Bourbon Argos’s staff but thanks to the sound security procedures enacted, all team members were safe. Nothing was taken during the incident and the damage to the ship was only minimal.”

The group added: “MSF strongly condemns this shameful act towards a humanitarian organisation rescuing and delivering lifesaving medical care to those crossing the central Mediterranean Sea.”

MSF has rescued more than 25,000 refugees from the southern Mediterranean over the past two years, and currently has three different boats operating off the coast of Libya. While the flow of refugees between Turkey and Greece has all but stopped, near-record numbers are still heading from Libya to Italy, and dying in the process. At least 3,100 are thought to have drowned so far this year, leaving MSF with a crucial lifesaving role in the southern Mediterranean.

More than 100,000 refugees have survived the journey and reached Italy in 2016, mainly fleeing war and poverty in Nigeria, and dictatorships in Eritrea and the Gambia. Sent to sea in dangerously flimsy inflatable boats, almost all of them have had to be rescued – either by European navies operating in the area, or by a fleet of humanitarian actors that now includes MSF, Save the Children, and the Migrant Offshore Aid Station (Moas).

On Thursday, Moas and MSF confirmed their missions would go ahead as planned while both groups assessed the security situation. Though both groups have long prepared for such incidents, last week’s raid is believed to be the first of its kind. During two separate reporting assignments on board the Argos, the Guardian was briefed on what to do in the event of a raid, and participated in security drills.

MSF said it was still assessing who might have been behind the raid, and analysts agreed it was hard to pinpoint who was responsible, given the complexity of Libya’s civil war.

The attackers seemed surprisingly well trained and well equipped, suggesting they came from some of Libya’s better-organised factions. “These were professionals, they were not just random fishermen,” said Argenziano. “They were trained in military tactics and [in the] use of weapons.”

There are dozens of militias operating along the Libyan coast, as well as special forces from several European countries including the UK, making identification difficult. Some militias are actively involved in the smuggling business, while others have tried to stop it – most effectively in the smuggling hub of Zuwara, where a masked militia is said to have forced most migrant smugglers to either down tools or switch to fuel smuggling.

Anas El Gomati, the director of the Libyan thinktank the Sadeq Institute, said it was unlikely that Islamic State, which is losing a battle for territory in central Libya, was behind the attack. “You can never rule out Isis, but it doesn’t have the signature PR [follow-up] that Isis goes for when they do these kinds of operations,” said El Gomati. “It also seems beyond Isis’s current capacities, given they are wedged into a war in central Libya.”

Argenziano said MSF would now spend two weeks assessing the situation before deciding on what long-term steps to take, but stressed that MSF’s commitment to lifesaving operations remained unchanged. “It is important to stress that we are an organisation specialised in working in emergencies and highly insecure contexts,” he said.

But Argenziano ruled out working under the direct protection of the European navies operating in the area, citing MSF’s history of acting independently of state actors. He also questioned the role of the naval operations, which are first and foremost meant to be anti-smuggling missions aimed at deterring future migration across the Mediterranean. “Is the deterrent bringing any of the intended results?” said Argenziano. “People keep on dying in large numbers, while the [arrival] numbers are not going down.”