"Perhaps we have avoided the worst," Interior Minister Brice Hortefeux told journalists, adding that investigators were trying to establish which targets in "France or elsewhere" the suspect was hoping to strike.
Security sources in Paris said the suspected Islamist, one of a pair of brothers detained on Thursday, worked at the European Organisation for Nuclear Research on the Franco-Swiss border just outside Geneva.
The pair were arrested in Vienne, a town on the Rhone river some 100 kilometres (65 miles) southwest of the Alpine lab, by officers from France's security service acting on a warrant from an anti-terrorist magistrate.
According to officials, the engineer had made contact over the Internet with Al-Qaeda in the Islamic Maghreb, a North African offshoot of Osama bin Laden's loosely organised global Islamist militant movement.
He had expressed a desire to carry out attacks, but had "not got to the stage of carrying out material acts of preparation", one said.
CERN confirmed a physicist working at the site had been arrested "under suspicion of links to terrorist organisations", and said it was helping the French police with their investigation.
"He was not a CERN employee and performed his research under a contract with an outside institute. His work did not bring him into contact with anything that could be used for terrorism," it added in a statement.
According to a report on the newspaper Le Figaro's website, the suspects are a 32-year-old Frenchman of Algerian origin who has been the subject of a police inquiry for a year-and-a-half and his 25-year-old brother.
The report, citing sources close to the inquiry, said the elder brother had had several Internet exchanges with figures considered close to Al-Qaeda and had provided a list of suggested French targets for attack.
Judicial sources told AFP that investigators had come upon the pair while monitoring the Internet as part of a separate inquiry into the recruitment of would-be jihadists to send to Afghanistan as guerrillas.
Intelligence agents recorded several incriminating exchanges between the brothers and suspected Al-Qaeda contacts. Two laptops, three hard drives and several USD memory sticks were seized from their home, they said.
"We are in a situation of permanent alert. We follow statements made by the leaders of certain organisations day by day. We never let our guard down. The danger is permanent," Hortefeux said.
Al-Qaeda in the Islamic Maghreb was born in 2007 when a largely-Algerian militant group, the Salafist Group for Preaching and Combat, swore allegiance to Bin Laden and rebranded itself as his organisation's local franchise.
Intelligence officials consider it one of the most serious threats to France, which has a large North African diaspora population.
CERN is Europe's leading laboratory for the study of the fundamentals of sub-atomic physics. It operates particle accelerators to study the behaviour of atoms at high speed and learn about the basic laws of nature.
It is a civilian organisation, backed by 20 member states, and is not connected to nuclear weapons technology.
The lab said the suspect had been working on the "LHCb experiment" which its website says "will help us to understand why we live in a universe that appears to be composed almost entirely of matter, but no antimatter.
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