Additionally, wreckage from the Airbus A320's front section showed "signs of high temperature damage and soot," the ministry said in a statement.
What caused the plane carrying 56 passengers and 10 crew members to plunge to the sea on May 19 remains a mystery, but the latest information could bring investigators closer to determining a cause.
"We now know that there was some form of either smoldering or some form of fire or some form of combustion, if you like, on that plane, and that has been verified," CNN aviation analyst Richard Quest said.
The recorded data was consistent with information from the Aircraft Communications Addressing and Reporting System
, or ACARS -- which sends messages between planes and ground facilities -- indicating "lavatory smoke and avionics smoke," according to the ministry.
"Analysis will be carried out to try to identify the source and reason for those signs," the statement said.
Evidence from the wreckage will enable investigators to build a forensic picture of what occurred.
"We will know whether this was a bomb or whether it was a fire," Quest said.
The flight data recorder holds 25 hours of technical information from plane sensors, including air speed, altitude, engine performance and wing positions. The cockpit voice recorder captures flight deck sounds, including crew conversation, alarms and background noises.
Authorities are still trying to repair the voice recorder's damaged memory chip
at the French version of the U.S. National Transportation Safety Board.
The so-called black boxes offer the best clues to determining why the plane went down while en route from Paris to Cairo.
"This is an amazing development taking us ever closer to learning what happened," Quest said of the new evidence. "We can't say whether it was nefarious or mechanical."
The flight was at 37,000 feet when it lost contact
above the Mediterranean, shortly before the aircraft entered Egyptian airspace. Then, the FDR stopped recording.
"That's significant," Quest said. "What that tells me is that whatever happened to the plane, happened at that altitude. It was dramatic. It was sudden and the plane then plunged."
In the hours that followed the disappearance, Egyptian officials said it was far more likely that a terrorist attack brought down the plane, than a technical fault.
But they didn't elaborate, or present evidence for that claim.
To this day, there has been no claim of responsibility by any terrorist organization.
The black boxes were recovered by the crew of the John Lethbridge, a privately owned deep-sea survey and recovery vehicle contracted by Egypt's government to aid in the search.
Crews are continuing to search for wreckage and the victims' remains.
Egypt's military also spotting wreckage, personal belongings
including an uninflated life vest, a seat, a purse, shoes, carpet, a scarf, parts of chairs and cushions and a sling bag. The EgyptAir label appeared on one piece of wreckage.