The 58-year-old man was taken into custody by border police upon his return to France while his wife was also being questioned as a witness, a day after their flight from Mauritius to Paris was diverted to Kenya.
The source gave no further details about the couple, including their nationalities.
A passenger alerted crew members to the device found inside a toilet cubicle on Sunday on board the Boeing 777, which was carrying 459 passengers and 14 crew.
The object, made up of cardboard, paper and a kitchen timer, was found to pose no danger to the aircraft or its passengers, Air France chief executive Frederic Gagey said yesterday.
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He said the "deduction" was that the item had been placed in a toilet cupboard by one of the passengers and said the bomb scare appeared to be the result of a "bad joke".
Several passengers were questioned in Mombasa before a plane was sent to return all those on board to France.
The airline "filed a legal complaint against unknown persons for endangering the life of others," the spokesman said.
France is on high alert after jihadist attacks in Paris in November left 130 people dead, and is one of many countries taking extra security precautions.
Airlines are especially jittery after Islamic State jihadists who claimed the Paris attacks also said they were responsible for downing a Russian jet in Egypt in October after smuggling a bomb onto the plane, killing all 224 people on board.
Mauritian Prime Minister Xavier Luc Duval told AFP airport security in the country had been boosted as a "precaution".
"All procedures at the airport have been reviewed and it was confirmed that they are scrupulously respected," Duval said after he met with security and airport chiefs.
Air France's chief executive Gagey said the object was found "in a small cupboard behind the mirror" in the toilet.
He said the bits of cardboard and paper and what "appeared to be a kitchen timer" were not items normally found on board.