"For me it is not true," Safwat Musallam said on the sidelines of the International Air Transport Association (IATA) annual meeting in Dublin.
He said flight MS804 had not experienced any maintenance issues before departure and that the plane was "normal".
"We fully trust the aircraft and the pilot," said Mr Musallam.
The reports came a day after a French naval ship detected signals from one of the black box flight recorders from the missing EgyptAir plane that was en route from Paris to Cairo when it disappeared off radar screens and crashed in the early hours of May 19.
The discovery raises hopes that the data and cockpit voice recorders, known as black boxes, can soon be retrieved and will give insight into what caused the crash.
The search zone for the jet has now been narrowed to two kilometres (1.24 miles), an Egyptian source on the investigation committee said on Thursday.
But it will be at least a week before a specialist vessel carrying robots able to dive to 3,000 metres will arrive to help retrieve the devices in the crash area that lies around 180 miles north of the Egyptian port of Alexandria.
Nearly two weeks after the crash, the cause of the tragedy still has not been determined. Egypt's civil aviation minister, Sherif Fathi, has said he believes terrorism is a more likely explanation than equipment failure or some other catastrophic event.
But no hard evidence has emerged on the cause, and no militant group has claimed to have downed the jet.
Earlier, leaked flight data indicated a sensor had detected smoke in a lavatory and a fault in two of the plane's cockpit windows in the final moments of the flight.
