"There was just too much sand," said Cheryl Ward, an anthropologist at Florida State University in Tallahassee.
Then, last December, Ward and other archaeologists working at the site found pieces of the vessels in a set of six caverns.
Egyptian troops had likely hacked the caves into a sand-covered bluff for use as storerooms and workrooms.
The planks had been salvaged from decommissioned vessels as building materials for the caverns.
There is no doubt that the planks are from oceangoing ships, Ward says, because they show damage from a type of wood-boring mollusk called a shipworm, which only lives in salt water.
And the extent of the damage indicates that the ships were in the water for several monthslong enough to make a journey of several thousand miles.
Between visits to Wadi Gawasis, the ancient Egyptians carefully closed everything up, like a mothballed military base. Eventually the sailors stopped visiting the site.
The Wadi Gawasis finds are revealing major insights into how the vessels were put together.
"They look like river ships, but scaled up," Ward said.
The ships, she says, were built with a type of joint known as mortise-and-tenon, which resembles a plug and its socket.
Such an assembly method would allow the ships to be hauled 90 miles (145 kilometers) across the desert in pieces, then put together at the port.
Inscriptions found in other parts of the Wadi Gawasis complex indicate that battalions of 3,700 men carried enough planks across the desert to make entire fleets of five or six ships at a time.
In addition to the ship remains, the caverns contained cargo boxes with inscriptions revealing that Punt had indeed been the vessels' destination.
Nobody is sure where Punt was located. But the trip there would probably have followed the coast rather than striking out across any large expanses of open water.
That's because the Egyptians, at home on the waters of the Nile, were not great ocean navigators.
"Wherever possible they followed the coast," Snape, of the University of Liverpool, said. "But they were willing to go long distances to get the things they required."
At other points in their civilization, Snape says, the ancient Egyptians even went as far as equatorial Africa for ostrich eggs and animal skins.
Most likely, Punt lay somewhere in modern Eritrea or Yemen.
Other researchers from Boston University and the University of Naples are scouring the Red Sea shore for additional traces of Egyptian shipping that might give better hints to the ancient sailors' destination.
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