Refugee charities are paying people smugglers to ferry migrants to their rescue boats patrolling off Libya, it was claimed last night.

A senior Libyan coastguard official told The Mail on Sunday he had evidence that aid agencies were stumping up cash for migrants desperate to reach Europe but who cannot afford to pay ruthless traffickers.

Colonel Tarek Shanboor said he had obtained bank details and phone records that proved the charities were making payments to criminal gangs who have put hundreds of thousands of migrants into unseaworthy boats – leading to thousands of deaths each year.

His claim will raise concern because there have long been fears that Islamic extremists could be among the migrants.

Col Shanboor said that in a desperate effort to stamp out the smuggling trade once and for all he had resorted to hiring a Tripoli- based militia to patrol the coast with his police force

Charities patrolling off northern Africa claim they are only there to rescue migrants.

But Colonel Shanboor said aid agencies were now encouraging more and more migrants to make the perilous trip. He claimed he had handed evidence of collusion between charities and traffickers to EU border security officials in Brussels, though he refused to go into detail.

Speaking exclusively to the MoS he said: ‘The non-governmental organisations (NGOs) are adding to the crisis by actively encouraging increasing numbers of migrants. Now we have the evidence they are in cahoots with the smugglers. We have evidence the smugglers call the NGOs directly and there are business deals between them.’

Col Shanboor claimed charities were paying up £450 for each migrant’s passage. He believes their motives are well-meaning but misguided.

Col Shanboor’s extraordinary accusation comes just months after an internal EU report revealed charity officials in boats were in direct contact with migrant vessels and even gave them precise directions to find rescue vessels. This year has already seen record numbers of migrants attempting the perilous crossing from Libya to Lampedusa and Sicily, turning Italy into the front line of the crisis.

A Sicilian prosecutor has launched an investigation into alleged collusion between traffickers and charities and accused NGOs of fuelling the migrant crisis in Europe.

Last month, about 1,500 migrants – among them hundreds of children and pregnant women – were rescued from rickety vessels by one of the charities, Medecins Sans Frontieres (MSF). And a leaked intelligence report suggested more than six million asylum seekers, including Syrians fleeing civil war, are waiting to cross into Europe.

The huge surge has led to more than 1,200 deaths already this year as smuggling gangs in lawless Libya resort to increasingly underhand tactics. According to the Ministry of Defence, the British Navy has rescued 14,900 migrants in total as part of the EU effort to crack down on the people smuggling trade.

Since 2014, when the EU’s maritime efforts shifted from search and rescue to border control, charities have deployed dozens of their own missions to fill the gap.

Charities including Save the Children and MSF argue their operations save lives near the coast, but critics including the Libyan coastguard say search and rescue encourages traffickers and has transformed the central Mediterranean into a magnet for migrants.

In a report last year, the EU border agency Frontex claimed ‘all parties involved in search and rescue operations in the central Mediterranean unintentionally help criminals achieve their objectives at minimum cost [and] strengthen their business model by increasing the chances of success’.

In another leaked document, Frontex reported the ‘first case where the criminal networks were smuggling migrants directly on an NGO vessel’ and a separate case where it said migrants were given ‘clear indications before departure on the precise direction to be followed in order to reach the NGOs’ boats’.

Charities including Save the Children and MSF argue their operations save lives near the coast, but critics including the Libyan coastguard say search and rescue encourages traffickers and has transformed the central Mediterranean into a magnet for migrants

A Frontex spokesman told this newspaper there had even been one occasion when a charity boat used its light as a beacon for migrants heading to Europe, but said it had no evidence smugglers were being paid by charities.

Meanwhile, Carmelo Zuccaro, a Sicilian magistrate, has launched an investigation into collusion between traffickers and charities and said he was collecting evidence of criminality.

Col Shanboor said that in a desperate effort to stamp out the smuggling trade once and for all he had resorted to hiring a Tripoli- based militia to patrol the coast with his police force.

‘This is a last-ditch attempt to stop the criminal trade along our coast. The Tajoura fighters should be able to dismantle the mafia groups. We are declaring war on the people smugglers this way,’ he said.

Last night, charities operating in the central Mediterranean all denied claims they had any contact with smugglers and dismissed suggestions of payment.

A spokesman for Migrant Offshore Aid Station (MOAS), which was launched by a philanthropist millionaire couple in 2014, said: ‘MOAS conducts rigorous due diligence on donors, sponsors and partners and abides by codes of ethical fundraising when dealing with both national and private sources of funding.’

Julien Pahlke, a spokesman for Dutch charity Jugend Rettet, which has one rescue boat off the Libyan coast, said: This is entirely false and sounds like attempts to damage our reputation and vilify us. We have never had any contact with smugglers and we would never cooperate with them.

‘They see us as enemies because they think we’re fuelling the crisis. But the EU is not heavily involved in rescue so migrants see us as the key to get to Europe.’

Sea-Watch, a German charity with two rescue boats in the Mediterranean, described the claims as ‘ridiculous’. MSF and Save the Children, both of which have launched hundreds of rescue operations in the Mediterranean, denied the claims.

MSF search and rescue coordinator Michele Trainiti said: ‘MSF does not have any contact, negotiations or exchange with smuggling networks anywhere. MSF search and rescue boats do not receive alerts or distress calls from smugglers and never have.’

A spokesman for Save the Children said: ‘We do not communicate with traffickers or people smugglers and believe all issues of security and trafficking need to be handled by the relevant European authorities. We do not pay smugglers for migrants. Additionally, we work under the co-ordination of the Italian coastguard and have no direct contact with vessels in distress. We operate in international waters, moving closer to territorial waters only if instructed by the Italian coastguard.’