The EU justice commissioner spoke of the number of jihadists being recruited in Europe on the eve of a Barcelona meeting of European and North African foreign ministers.
Representatives from 36 countries will meet in the Catalan capital to discuss ways to fight terrorism.
"At the European level, we estimate that 5,000 to 6,000 individuals have left for Syria," Věra Jourová told Le Figaro in an interview, adding that the true number was likely to be far higher due to the difficulty of tracking foreign fighters in the conflict.
"At the time of the attacks in Paris and Copenhagen, we decided not to allow ourselves to be guided by fear," she said, referring to January's twin Islamist attacks in the French capital and the subsequent deadly shootings on a cultural centre in Denmark.
Focusing on those seeking to leave for Syria to wage jihad, or those returning from the conflict, meant intervening "too late", she said.
Jourová said the EU instead wanted to promote prevention as a means of curtailing the steady flow of European nationals, looking at the diverse reasons of why people joined jihadist groups beyond simply religion.
Her comments came just days after police arrested a cell in Catalonia that was poised to carry out an attack.
The 11 suspected terrorists arrested last week across the northeastern region planned to carry out kidnappings and a public execution, as well as attacks on Jewish businesses, according to a judge who questioned them.
British research had identified "a desire for adventure, boredom, dissatisfaction with their situation in life or a lack of prospects," in those who had opted to leave their families behind and head for Syria, the commissioner said.
Another focus for the EU was speeding up the exchange of information between the police forces and court systems of member states, she said, with more intelligence sharing required.
The self-proclaimed Islamic State, which rules a swathe of territory in Syria and Iraq it has deemed an Islamic "caliphate", has attracted thousands of foreign fighters, many from the West.
Authorities have reported that about 100 Spaniards have travelled to join jihadists in Iraq and Syria.
Still, this number is relatively low compared to Spain's western European counterparts, according to the International Centre for the Study of Radicalisation and Political Violence (ICSR).
The ICSR's most recent estimates showed that while France, Germany and the United Kingdom have seen the highest number of residents and citizens leaving to join fighters in Syria and Iraq, Belgium, Denmark and Sweden have been most affected per capita.
Spain has stepped up anti-terrorism efforts in recent months, conducting a series of raids on suspected jihadist cells, though most of those arrested have been accused of recruiting militants for Isis fighters rather than actually planning attacks themselves.
Catalonia police arrested 11 people with suspected links to Isis last week for allegedly planning an attack in the region.
More than 215,000 people have been killed in Syria's four-year war, which is increasingly dominated by jihadist groups.