The development raised hopes the plane's flight data and cockpit voice recorders, known as the black boxes, could be retrieved and shed light on the aircraft's crash.
In Cairo, Egypt's Civil Aviation Ministry cited a statement from the committee investigating the crash as saying the vessel Laplace received the signals. The French Navy confirmed the Laplace arrived on Tuesday in the search area and picked up the signals "overnight".
The signals' frequencies could match with the frequencies of data recorders, a French Navy spokesman said. The location and identification of the source of the signals have not been determined yet, he said, adding that the searches are still at an "early stage".
Laplace's equipment picked up the "signals from the seabed of the wreckage search area, assumed to be from one of the data recorders," the Egyptian statement read. It added that a second ship, John Lethbridge affiliated with the Deep Ocean Search firm, will join the search team later this week.
Locator pings emitted by flight data and cockpit voice recorders, known as the black boxes, can be picked up from deep under water. The Laplace is equipped with three detectors designed to detect and localise signals from the flight recorders, which are believed to be at a depth of about 3,000 meters under water.
Shaker Kelada, an EgyptAir official who has led other crash investigations for the carrier, said half "the job has been done now" and that the next step would be to determine the black boxers' exact location and extract them from the sea.
"We have to find where the boxes are exactly and decide on how to pull them out," he said, adding that search teams might need to send in robots or submarines and "be extremely careful ... to avoid any possible damage".
Mr Kelada said he was confident the boxes will be retrieved. He had investigated the Flash Airlines Flight 604 crash in 2004, when the aircraft hit the Red Sea shortly after take-off from the resort of Sharm el-Sheikh, killing all 148 passengers, most of them French tourists, and crew on board.
In the May 19 crash, EgyptAir Airbus A320 had been cruising normally in clear skies on a nighttime flight to from Paris to Cairo when it suddenly lurched left, then right, spinning all the way around and plummeting 38,000 feet into the sea, Greek Defence Minister Panos Kammenos said shortly after the crash.
However, Egyptian authorities refuted this, saying that the plane did not swerve or lose altitude before it disappeared off radar. A distress signal was never issued, EgyptAir said.
Since the crash, small pieces of the wreckage and human remains have been recovered while the bulk of the plane and the bodies of the passengers are believed to be deep under the sea. A Cairo forensic team has received the human remains and is carrying DNA tests to identify the victims. The search has narrowed down to a 3-mile area in the Mediterranean.
David Learmount, a consulting editor at the aviation news website Flightglobal, said the black boxes' batteries can transmit signals up to 30 days after the crash. But even if the batteries expire, locating the boxes remains a possibility.
"It's terribly important to find the black boxes, because if they don't find them, they will know nothing about the aircraft," he said, citing a 2009 incident when black boxes were found two years after a crash in the Atlantic Ocean.
Nearly two weeks after the crash off Egypt's northern coast, the cause of the tragedy has still 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 toilet and a fault in two of the plane's cockpit windows in the final moments of the flight.
In France, the country's air accident investigation agency could not immediately comment on the developments since they have not yet received any "official communication" from Egyptian authorities.