The decision, taken at a meeting of EU interior ministers, was announced by Rihards Kozlovskis, Latvia's interior minister, who chaired the session.
EU officials said the decision, to go into effect in June, will apply throughout the 26-nation Schengen area, to which 22 EU member states belong.
Kozlovskis said the "risk indicators" to be used to single out travelers and their documents for intensive examination are still being drafted by EU officials and member countries.
"The number of foreign fighters, unfortunately, keeps increasing quite dramatically," Kozlovskis said. "We have to do something to limit the movement of such persons. Unfortunately they are EU citizens, mostly."
Bloc officials have said the criteria employed to flag travelers probably will not involve ethnic origin or related factors, such as which airline passengers order special meals meeting religious dietary restrictions, but would include their destination or complete itinerary.
The EU made fighting terrorism a top priority after the Jan. 7-9 attacks in Paris that claimed 17 victims. French Interior Minister Bernard Cazeneuve, who represented his country's government at Thursday's meeting in Brussels, urged decisive and speedy action.
"Today the fight against terrorism is a fight against time," Cazeneuve told reporters. "It's a fight against the clock. And each minute we lose by procrastinating is an additional opportunity that we give to the terrorists to strike."
According to one estimate, some 4,000 Europeans have left to fight alongside radical Muslim formations in Syria and Iraq since October.
EU goverments want to prevent them from departing, and also catch them if they return home with the intent of staging terrorist attacks on their home soil.
Ministers also discussed how their nations could better share information in the terrorism area and stem the illegal trafficking in firearms.
At a closing press conference, Kozlovskis said the meeting also considered a proposal that everyone entering or leaving the Schengen area should have their passports checked electronically against databases, but no follow-up action was taken.
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