The navy had identified two separate "pinging sounds", 15ft away from each other, on the sea bed 250ft (78 metres) below USS Grapple, coming from the cockpit voice recorder and the flight data recorder of the jet that crashed into the Atlantic off Nantucket, Massachusetts, on Sunday.
The ship's crew launched a camera-equipped, deep-diving robot which was clawing its way through the silt in an attempt to reach the recorders.
The Remote Operating Vehicle (ROV), or Deep Drone, is equipped with sonar, still and television cameras. But the crew operating it had little time to recover the black boxes as the National Weather Service forecast gale force winds and heavy seas would strike the search area, some 60 miles (100km) off the Massachusetts coast. The hunt has already been delayed for two days by bad weather. Winds were forecast to reach more than 30 knots creating waves of up to 12ft last night and a Navy spokesmen said neither divers nor the hi-tech submersible robot could operate under such conditions.
Investigators hope the black boxes will help explain what happened to the Boeing 767-300ER aircraft that crashed on Sunday minutes after takeoff from New York en route to Cairo, killing all 217 people on board.
As the salvage operation struggled with the weather, commemorative prayers were being held at mosques throughout Egypt.
"Life is not void of struggles or crises or situations which sadden man, but we must accept the will of God Almighty with patience," Mohammad Sayed Tantawy, grand sheikh of Al-Azhar, a Cairo-based seat of learning revered across the Sunni Moslem world, said in his sermon prior to the prayers.
While families of the victims of EgyptAir Flight 990 struggled with their grief, whispered conspiracy theories on the cause of the crash were doing the rounds in Cairo. Opinions ranged from an Israeli-injected virus on the aircraft's on-board computer to a United States-fired surface-to-air missile.
There have even been suggestions that the crash was linked to Egypt's new government taking office. Since the cabinet's inauguration last month, Egypt has been beset by a string of misfortunes, an opposition newspaper pointed out Friday.
Egypt, like the rest of the Middle East, is no stranger to unsubstantiated conspiracy theories. Israel is often the alleged culprit.
At a fashionable cafe in the affluent Cairo suburb of Heliopolis, a group of young men sat riveted on Thursday as their friend, Ibrahim Sameh, 34, gave his take on Sunday's crash of the EgyptAir Boeing 767.
"An Israeli agent on board the plane used a portable computer to install a virus into the plane's navigation system," the accountant declared. His motive? To kill the 33 Egyptian military officers on board.
They were "important" officials, Mr Sameh said. "In this way, they could undermine our national security without having fired a single bullet."
Nor has America escaped the glare of public doubt. Pointing out that the US has not ruled out the possibility of a surface-to-air missile fired from a nearby base, Samir Ragab, editor of the pro-government Egyptian Gazette newspaper, wrote that "sometimes, such firing could happen by mistake."