One plot involved a staggering four tons of the illegal drug with a street value of £168million.
Al Qaeda, led by 9/11 mastermind Osama bin Laden until his death in May 2011, is using profits to fund terror plots in the UK and western Europe.
And they have paid for the cocaine with weapons looted in Libya during the mayhem following the death of Colonel Gaddafi in 2011.
Spooks from MI6 and the UK’s criminal intelligence agency SOCA have joined forces to investigate al Qaeda’s links to drug cartels and terrorist groups in Africa and South America.
Two Colombians – one a member of left-wing terror movement FARC – were arrested after a probe by the US Drugs Enforcement Agency.
It is understood the South American group, now a major cocaine cartel, sold a large quantity of the drug to bin Laden’s North African branch, al Qaeda of the Islamic Maghreb.
They paid using cash and also weapons looted in Libya.
The drug was shipped to North Africa and moved across the Mediterranean into southern France where it is believed to have been distributed to other European countries, including the UK.
A second operation carried out by secret intelligence groups led to the arrest of the former head of the navy in West Africa’s Guinea-Bissau, now classed as a “narco-state” because of its reliance on the cocaine trade.
Admiral Jose Americo Bubo Na Tchuto and six others have now been flown to New York and charged with drugs trafficking. Four also face terrorism charges.
They were caught in a sting operation in which they believed they were talking to members of FARC. They agreed to supply ground-to-air missiles and a quantity of AK-47 assault rifles and grenade launchers in exchange for four tons of cocaine with a street value of £168million.
Al Qaeda of the Islamic Maghreb has long been involved with cocaine traffickers, receiving large payments to ensure drug runners could safely cross the Algerian Sahara with multi-million-pound consignments.
But spies say this is the first time evidence has emerged suggesting the organisation are themselves trafficking cocaine into Europe.
A highly placed crime intelligence source in London said: “It is a very worrying development and both MI6 and SOCA will be working together to find out as much as they can.
“When there is an overlap between straightforward crime and security matters, the two agencies work together. There will be a lot of interaction with security forces from several countries.
“France will be particularly involved given the Algerian connection and the fact that France seems to be the main entry point for the al Qaeda shipments. There will also be strong American interest.’’
In January 2009 Briton Edwin Dyer, 60, was kidnapped by al Qaeda of the Islamic Maghreb while holidaying in Niger.
He was held hostage for five months before being beheaded in neighbouring Mali, where his captors have vowed to set up “an Afghanistan in Africa” despite a French military operation to kick them out.
Meanwhile in Afghanistan the Taliban announced the start of their spring offensive. Almost 500 people, including 217 insurgents, have already been killed there this month.