French magistrates on Monday charged Adlene Hicheur, a 32-year-old researcher at the Swiss Federal Institute of Technology (EPLF) in Lausanne, Switzerland, with "membership of a terrorist group."
Investigators monitored Internet messages between the scientist and a north African off-shoot of Al Qaeda, French officials said.
Halim Hicheur, 30, said his brother frequently sent emails to people in Algeria, but said there had been no correspondence with the terrorist group.
"Most of my family is from Algeria," the brother told the journal Nature, insisting that there was nothing in the family background "that would have made us think about violence."
"We are Muslims, we have never hidden this," he added.
Adlene Hicheur was working under contract at the European Organisation for Nuclear Research (CERN) when he was arrested.
Halim also denied that he had been taken into custody along with his brother, as was widely reported in the media.
"I have never been contacted by the police," he said, explaining that it was his youngest brother who was picked up and later released without charge on October 10.
Halim told Nature that his scientist brother, just before his arrest, had withdrawn 13,000 euros (19,200 dollars) for a land purchase near their ancestral home in Algeria.
Police asked questions about the money, which may have sparked the arrest, he suggested.
CERN operates one of the world's leading nuclear research laboratories attached to a 27-kilometre (15-mile) tunnel running under the Franco-Swiss border just outside Geneva.
In the tunnel, a particle accelerator attempts to recreate the sub-atomic conditions present at the time of the Big Bang.