Gunmen have attacked a charity-funded boat rescuing refugees in the Mediterranean Sea, shooting at international aid workers before boarding the vessel.

The Bourbon Argos, which is operated by Doctors Without Borders (MSF), was patrolling around 24 nautical miles north of the Libyan coast when a speedboat approached.

Those on board failed to identify themselves or answer radio contact, then opened fire from around 500 metres away as rescue workers sought refuge in a designated safe area.

The armed men then boarded the Bourbon Argos and searched the vessel, which had no refugees on board at the time, for almost an hour.

A doctor carries a child as refugees disembark from the Medecins Sans Frontieres (MSF) vessel at Pozzallo's harbour in Sicily, Italy (Reuters)

MSF said they did not steal or remove anything and left minimal damage, although staff emerged to find bullet holes in the ship.

“Although we don’t know the identity of the attackers or their motivation, our initial assessment of the facts shows that they were professional and well-trained,” said Stefano Argenziano, MSF’s operations co-ordinator.

“This was a serious and worrying attack, with shooting toward our boat which could have put our staff in acute physical danger.”

The attack on 17 August was believed to be the first of its kind in the refugee crisis, where several naval and humanitarian ships are patrolling the Mediterranean and Aegean seas in efforts to prevent boat disasters that have killed more than 3,000 asylum seekers so far this year.

Desperate journeys: Rescued at sea, refugees detail abuse in Libya

The main launching point is the north-western coast of Libya, where instability and lawlessness since the country’s civil war has enabled smuggling gangs to set up a ruthless and profitable trade.

Libya's fragile government is struggling to stop warring militias battling for territory after years of chaos and prevent the spread of Isis, which has recently been driven out of the city of Sirte with the aid of British and American special forces and air strikes.

The so-called Islamic State is considered an unlikely culprit for the attack on the Bourbon Argos, which is a more probable target for gangs looking to extort refugees on board.

The Central Mediterranean has become the deadliest sea crossing in the world, with traffickers frequently forcing untrained migrants to sail unseaworthy and overcrowded vessels towards Italy.

Refugee crisis - in pictures Show all 27 1 /27 Refugee crisis - in pictures Refugee crisis - in pictures A child looks through the fence at the Moria detention camp for migrants and refugees at the island of Lesbos on May 24, 2016. AFP/Getty Images Refugee crisis - in pictures Ahmad Zarour, 32, from Syria, reacts after his rescue by MOAS (Migrant Offshore Aid Station) while attempting to reach the Greek island of Agathonisi, Dodecanese, southeastern Agean Sea Refugee crisis - in pictures Syrian migrants holding life vests gather onto a pebble beach in the Yesil liman district of Canakkale, northwestern Turkey, after being stopped by Turkish police in their attempt to reach the Greek island of Lesbos on 29 January 2016. Getty Images Refugee crisis - in pictures Refugees flash the 'V for victory' sign during a demonstration as they block the Greek-Macedonian border Refugee crisis - in pictures Migrants have been braving sub zero temperatures as they cross the border from Macedonia into Serbia. Refugee crisis - in pictures A sinking boat is seen behind a Turkish gendarme off the coast of Canakkale's Bademli district on January 30, 2016. At least 33 migrants drowned on January 30 when their boat sank in the Aegean Sea while trying to cross from Turkey to Greece. Getty Images Refugee crisis - in pictures A general view of a shelter for migrants inside a hangar of the former Tempelhof airport in Berlin, Germany Refugee crisis - in pictures Refugees protest behind a fence against restrictions limiting passage at the Greek-Macedonian border, near Gevgelija. Since last week, Macedonia has restricted passage to northern Europe to only Syrians, Iraqis and Afghans who are considered war refugees. All other nationalities are deemed economic migrants and told to turn back. Macedonia has finished building a fence on its frontier with Greece becoming the latest country in Europe to build a border barrier aimed at checking the flow of refugees Refugee crisis - in pictures A father and his child wait after being caught by Turkish gendarme on 27 January 2016 at Canakkale's Kucukkuyu district Refugee crisis - in pictures Migrants make hand signals as they arrive into the southern Spanish port of Malaga on 27 January, 2016 after an inflatable boat carrying 55 Africans, seven of them women and six chidren, was rescued by the Spanish coast guard off the Spanish coast. Refugee crisis - in pictures A refugee holds two children as dozens arrive on an overcrowded boat on the Greek island of Lesbos Refugee crisis - in pictures A child, covered by emergency blankets, reacts as she arrives, with other refugees and migrants, on the Greek island of Lesbos, At least five migrants including three children, died after four boats sank between Turkey and Greece, as rescue workers searched the sea for dozens more, the Greek coastguard said Refugee crisis - in pictures Migrants wait under outside the Moria registration camp on the Lesbos. Over 400,000 people have landed on Greek islands from neighbouring Turkey since the beginning of the year Refugee crisis - in pictures The bodies of Christian refugees are buried separately from Muslim refugees at the Agios Panteleimonas cemetery in Mytilene, Lesbos Refugee crisis - in pictures Macedonian police officers control a crowd of refugees as they prepare to enter a camp after crossing the Greek border into Macedonia near Gevgelija Getty Images Refugee crisis - in pictures A refugee tries to force the entry to a camp as Macedonian police officers control a crowd after crossing the Greek border into Macedonia near Gevgelija Getty Images Refugee crisis - in pictures Refugees are seen aboard a Turkish fishing boat as they arrive on the Greek island of Lesbos after crossing a part of the Aegean Sea from the Turkish coast to Lesbos Reuters Refugee crisis - in pictures An elderly woman sings a lullaby to baby on a beach after arriving with other refugees on the Greek island of Lesbos after crossing the Aegean sea from Turkey Getty Images Refugee crisis - in pictures A man collapses as refugees make land from an overloaded rubber dinghy after crossing the Aegean see from Turkey, at the island of Lesbos EPA Refugee crisis - in pictures A girl reacts as refugees arrive by boat on the Greek island of Lesbos after crossing the Aegean sea from Turkey Getty Images Refugee crisis - in pictures Refugees make a show of hands as they queue after crossing the Greek border into Macedonia near Gevgelija Getty Images Refugee crisis - in pictures People help a wheelchair user board a train with others, heading towards Serbia, at the transit camp for refugees near the southern Macedonian town of Gevgelija AP Refugee crisis - in pictures Refugees board a train, after crossing the Greek-Macedonian border, near Gevgelija. Macedonia is a key transit country in the Balkans migration route into the EU, with thousands of asylum seekers - many of them from Syria, Afghanistan, Iraq and Somalia - entering the country every day Getty Images Refugee crisis - in pictures An aerial picture shows the "New Jungle" refugee camp where some 3,500 people live while they attempt to enter Britain, near the port of Calais, northern France Getty Images Refugee crisis - in pictures A Syrian girl reacts as she helped by a volunteer upon her arrival from Turkey on the Greek island of Lesbos, after having crossed the Aegean Sea EPA Refugee crisis - in pictures Refugees arrive by boat on the Greek island of Lesbos after crossing the Aegean sea from Turkey Getty Images Refugee crisis - in pictures Beds ready for use for migrants and refugees are prepared at a processing center on January 27, 2016 in Passau, Germany. The flow of migrants arriving in Passau has dropped to between 500 and 1,000 per day, down significantly from last November, when in the same region up to 6,000 migrants were arriving daily.

MSF said it would not withdraw three ships carrying its teams in the region and vowed to continue its work to save people fleeing armed conflict, persecution and extreme poverty.

The charities SOS Méditerranée and Migrant Offshore Aid Station are also carrying on their search and rescue missions, having prepared for the possibility of attacks at sea.

Mr Argenziano hit out at the “inadequate” response to the crisis by the EU, reiterating calls for safe and legal routes to Europe for those seeking safety.

“With the number of deaths continuing to dramatically increase and the deteriorating situation in Libya, we continue to consider the European focus on deterrence and security dangerously myopic and completely inadequate to respond to this crisis,” he added.