Investigators were picked up by the French vessel Laplace as it was searching the Mediterranean Sea.
There were 66 people on board when the Airbus A320 crashed on May 19 while flying from Paris to Cairo.
The plane vanished from Greek and Egyptian radar screens, apparently without having sent a distress call.
Remi Jouty of France’s Bureau of Investigations and Analysis said: “The signal from a beacon from a flight recorder has been detected.”
A priority search area has been established, he added.
The French navy is awaiting the arrival of a second vessel that is equipped to take pictures and retrieve objects from the sea.
Egyptian investigators first reported that the French vessels had picked up signals from the wreckage search area, saying they were “assumed” to be from one of the devices.
Officials from Egypt said last week signals from the plane’s emergency beacon had been detected but later said they were received on the day of the crash and were not new.
What caused the crash remains a mystery. Finding the black boxes is crucial to piecing together what happened in the plane’s final moments.
Black boxes emit signals for 30 days after a crash, giving search teams an ever-narrowing window to locate them before their batteries run out.
Debris from the plane has been recovered from the sea, some 180 miles north of the Egyptian port city of Alexandria.
However, the bulk of the plane and the bodies of passengers are thought to be deep under the sea.
Those on board MS804 included 30 Egyptians, 15 French citizens, two Canadians, two Iraqis and citizens from Algeria, Belgium, Britain, Chad, Portugal, Saudi Arabia and Sudan.
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