The 735ft cargo vessel and its crew have been missing since issuing a distress call on October 1.
Search planes have found debris including life jackets, containers and oil in the water, but only one body has been recovered.
It is not clear why the captain decided to lead the ship into waters near Hurricane Joaquin.
“We were very saddened to learn that no survivors have been found,” said Bella Dinh-Zarr, vice chairman of the National Transportation Safety Board (NTSB).
The search officially ended on October 7 at sunset.
“They did all they could in this search effort… our crews and aircrafts flew repeatedly into that storm,” Coast Guard Captain Mark Fedor said on the same day.
An empty, heavily damaged life boat was also found.
The coast guard said it searched 70,000 sq nautical miles attempting to find the crew of 28 Americans and five Poles.
The El Faro ship, which was travelling from Florida to Puerto Rico, was taking on water before it sank according to the distress call.
Its owners, Tote Maritime, say the ship lost power after its engines broke down.
Tote Maritime, said two vessels it dispatched to the scene had found a container “which appears to be from the El Faro”.
In a statement it said the crew were “equipped to handle situations such as changing weather.”
Hurricane Joaquin brought heavy rains to the Bahamas, damaging a number of houses.
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