The 32-year-old French scientist, of Algerian origin, is being held with his younger brother after being trailed, and bugged, by French anti-terrorist police for more than a year.
A judicial source told the newspaper Le Figaro: "This is very high level." The French Interior Minister, Brice Hortefeux, said that the investigation "may perhaps show that we have prevented the worst".
The scientist, who was not immediately named, was arrested alongside his brother near Lyons on Thursday on suspicion of having contacts with al-Qa'ida in the Islamic Maghreb, or Aqim. He was said to have been suspected of giving advice on possible nuclear targets within France.