Kenyan police spokesman Charles Owino said Air France Flight 463 was heading to Charles de Gaulle airport in Paris when the pilots of the Boeing 777 requested an emergency landing at Moi International Airport at 12.37am local time.
Mr Owino said the plane, carrying 459 passengers and 14 crew members, had left Mauritius at 9pm.
Bomb squad experts are investigating the device, thought to be an explosive.
All passengers were evacuated safely and the device removed, Mr Owino said.
The crew “requested an emergency landing when a device suspected to be an explosive was discovered in the lavatory”, Mr Owino said.
The airport was closed during the evacuation and search.
“The object, believed to be an explosive device, has successfully been retrieved from the aircraft,” said Kenya Airports Authority in a post on Twitter, adding that scheduled flights to Mombasa were disrupted during the interval but that normal operations have resumed.
“The plane just went down slowly, slowly, slowly, so we just realised probably something was wrong,” said a passenger who identified himself as Benoit Luchini, of Paris. He spoke to journalists after leaving the plane in Mombasa.
“The personnel of Air France was just great, they were just wonderful. So they keep everybody calm. We did not know what was happening,” said Mr Luchini.
“So we secured the seat belt to land in Mombasa because we thought it was a technical problem but actually it was not a technical problem. It was something in the toilet. Something wrong in the toilet, it could be a bomb.”
Air France said investigators are working to confirm whether the package found on Flight 463 contained explosives
The Air France spokeswoman said local authorities were also interviewing passengers. The airline has sent a substitute plane to pick up the passengers