The Egyptian investigation committee confirmed the find as the search continues to find the black boxes, which could detail exactly what happened to the jet, before their signal runs out.
The deep ocean search vessel John Lethbridge identified the main locations of the wreckage and provided the first images of wreckage to investigators.
A search team on board the ship, contracted by the Egyptian government, will draw a map of the wreckage's distribution spots.
The committee said in a statement the ship "had identified several main locations of the wreckage, accordingly the first images of the wreckage were provided to the investigation committee."
Flight MS804 plunged into the Mediterranean Sea with 66 people on board after taking off from Charles de Gaulle airport in Paris on route to Cairo on May 19.
Investigators are now examining photographs taken of the wreckage from the seabed.
It was not immediately known which parts of the plane had been found, nor whether the two black boxes were nearby.
The recorders, one for voice and another for data, were contained in the tail of the Airbus A320.
It is not yet known what caused the crash but investigators desperately searching for the black boxes hope the flight recorders will provide the answer.
The black boxes are designed to send out signals for 30 days after a crash, leaving the search team funtil June 24 to find the flight recorders in the Mediterranean, which is up to 3,000 metres deep.
Parts of the wreckage and some of the victims’ possessions have already been found.
Previously collected debris will also be handed over to the investigation committee after "standard procedures" are completed by prosecutors who are currently holding it for forensic evidence.
To recover the black boxes some 3,000 metres below the surface, investigators will need to pinpoint the signals to within a few metres and establish whether the pingers are still connected to the recorders.
Egypt’s aviation minister initially said the plane may have been brought down by a terror attack, but a technical failure was also likely.
No group has claimed responsibility for an attack.
Flight data pointed to the possibility of an explosion after a series of warnings indicating smoke had filled the cabin were sent out.
Debris and some human remains have already been found around 180 miles north of Alexandria, Egypt.
The plane lost contact while cruising at around 37,000ft and had just left Greek airspace.
There were 56 passengers, including Briton Richard Osman, and 10 crew on board.
A French search vessel, the Laplace, located signals form the seabed which could have come from the plane’s black box earlier this month.
The John Lethbridge, which was built in the 1960s, can search down to 6000m.
The ship’s side scan sonar can search large sections of the sea each day.
