Government adviser Abdul Basit Haroun said smugglers were hiding IS militants on boats filled with migrants.
He based his claim on conversations with boat owners in parts of North Africa controlled by the militants.
He alleged that IS was allowing them to continue their operations in exchange for 50% of their income.
The UN estimates that 60,000 people have already tried to cross the Mediterranean this year.
More than 1,800 people are feared to have died making the journey in often overcrowded and unseaworthy boats in 2015 - a 20-fold increase on the same period in 2014.
In an interview with BBC Radio 5 live Investigates, Mr Haroun said IS used "the boats for their people who they want to send to Europe as the European police don't know who is from IS and who is a normal refugee or not".
The militants often sat separately from the other migrants and were not scared of the crossing, he said, adding that they were "for IS - 100%".
Mr Haroun added that IS allowed boat owners to operate - but demanded a 50% cut of whatever they made from each ship.
Source: The UN refugee agency
Militants, migrants and the Med
How strong is IS in Libya?
He also suggested that the jihadists were planning ahead for future attacks in Europe.
Earlier this year, the EU's border control agency, Frontex, warned that it was "possible" that foreign fighters were using irregular migration routes to get into Europe.
IS - which controls large parts of Iraq and Syria - has been active in recent months in Libya, exploiting a power struggle between rival groups after the fall of Col Muammar Gaddafi.
In March, IS also claimed responsibility for the attack in Tunisia's capital Tunis, in which 22 people were killed.
Islamic State (IS) fighters are being smuggled into Europe by gangs in the Mediterranean, a Libyan official has told the BBC.