A passenger alerted crew members to the item found inside a toilet cubicle on board the Boeing 777, which was carrying 459 passengers and 14 crew members from Mauritius to Paris.
"After analysis it has been indicated that (the bomb scare) was a false alarm," Air France chief executive Frederic Gagey told a press conference in Paris.
"All the information we have at this stage shows that the object was not capable of causing an explosion that would damage the plane but was rather a mixture of cardboard, pieces of paper as well as a timer," he 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.
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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.
Gagey said there had been three bomb scares on Air France planes in the United States since the attacks.
But it made an emergency landing at Moi International Airport in Kenya's southern port city of Mombasa at 12:37 am (2137 GMT) "after a device suspected to be a bomb was discovered in the lavatory," police spokesman Charles Owino said.
"An emergency was prepared and it landed safely and all passengers evacuated."
When the plane landed, passenger John Stephen said crew members helped safely evacuate people using emergency slides.
"We don't know anything more about this bomb or not, but something that looked like a bomb was in the toilet."
Navy and police bomb experts were called in to determine if there were any explosives aboard the plane.
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.