The officials said two fighter planes that were already airborne responded and directed the pilot to a nearby airport. They spoke on condition of anonymity because of the sensitivity surrounding the Dimona nuclear reactor.
Israeli media said the man had flown into the area accidentally.
Foreign experts have concluded that Israel possesses a formidable nuclear arsenal based on pictures taken at the site two decades ago by a technician.
Israel maintains a policy it calls nuclear ambiguity, refusing to acknowledge whether it has atomic weapons.