Once ashore in countries such as Italy and Greece, there are fears that militants could evade detection by the authorities – and try to plot violent attacks.
Meanwhile, The Mail on Sunday can reveal that British Special Forces divers are poised to launch a series of daring operations along the Libyan coastline to destroy the ships used by traffickers.
Claims that IS terrorists are posing as refugees are made by a Libyan security adviser, Abdul Basit Haroun, who used to live in Britain.
A double agent who betrayed Al Qaeda secrets to MI5 says ISIS now running its own small, but well-organised people-trafficking operation.
Aimen Dean, now a security consultant, also tells the programme that he knows of two Egyptian brothers who reached Italy from the Libyan port city of Sirte.
They were accompanied on their journey by men who were fluent in Italian and French'.
The claims come ahead of a crucial meeting tomorrow at which European Ministers will consider plans for air and naval strikes against the Libyan people-smugglers, subject to UN approval.
Last night, it emerged that frogmen from the Special Boat Service are expected to deploy from an Astute class UK submarine, approach in small teams and attach sophisticated limpet mines to the traffickers' ships which can then be detonated remotely.
Defence sources said that these missions would be 'in play' in three to four weeks, by which time the UN is expected to have passed a resolution authorising military force to stamp out human trafficking.
This year alone, 1,600 people are believed to have drowned while crossing the Mediterranean. Traffickers charge up to £6,000 for passage from North Africa to Europe.