"Like all major humanitarian crises", the Syria conflict "has political aspects and consequences that can have devastating effects", Emma Bonino told reporters in Rome.
"If you consider displaced people, refugees and immigrants, we have millions of people moving around the southern Mediterranean," she said.
"We have many reasons to believe that among the women and children, there are also less friendly immigrants - ex-jihadists or members of Al-Qaeda."
"It is clear that uncontrolled landings on our shores have implications for the security of the European Union."
While Bonino underlined the war in Syria as the main reason for displacement, she said poverty in the Sahel, insecurity in Somalia and lawlessness in Libya added to the problem.
"In the absence of any control over its territory, Libya is today becoming a sort of freeway where anything gets through - weapons, drugs," she warned.
The EU has been examining proposals to beef up border surveillance and open up legal channels to reach Europe to deal with the boats packed with Syrian refugees that have been arriving in southern Italy.