Around 40 undercover French flying squad detectives are searching for Islamic State extremists who could be hidden among the hundreds of Arabs, Africans and Asians camped in and around the busy ferry terminal.
The team from an elite police unit which has smashed six people-smuggling networks this year alone are working closely with the French equivalents of MI5 and MI6.
News of the undercover anti-jihadi operation comes just days after Italian police arrested a suspected Islamist militant allegedly involved in the deadly terror attack at the Bardo museum in Tunis in March.
Abdelmajid Touil, 22, from Morocco arrived in Italy on a migrant boat, fuelling fears that other jihadists could reach Europe in the guise of asylum-seekers crossing from north Africa.
Steve Barbet, a spokesman for the local Prefect in Calais, revealed the work to counter the jihadi threat in the French port and people trafficking gangs.
He said: “There is full and complete vigilance in Calais with regard to threat by jihadists or other criminal networks with potential involvement in people smuggling.
“All our resources are being directed towards detecting and eradicating any network whatsoever. Our priorities are the networks, the individual smugglers and the jihadist potential threat.”
Mr Barbet made his comments the day after the theft of a mobile phone sparked a mass brawl between about 200 Sudanese and Afghans at the new Sangatte camp at Calais.
Witnesses described seeing men armed with knives and iron bars setting about each other and metal barriers being hurled. Fourteen rioters were injured, eight seriously.
A team of 40 riot police was sent into a recently opened camp just outside the town to quell the fighting on Sunday.
Only women and children can stay inside the former holiday camp.
But, around 1,000 migrant men are living in make-shift tents in the dunes surrounding the camp and use its showers, kitchens and phone chargers on a daily basis.
Official estimates put the number of migrants currently in Calais and the surrounding area at 2,300 with 1,000 police, including UK Border Control officers, to control them.
But charity groups working with the squatters put the figure at closer to 3,000 with between 50 and 150 new arrivals every day.