En route from Florida to Puerto Rico, the 735-foot (224-meter) cargo ship was reported to be caught in the storm near Crooked Island, which is part of the Bahamas.
In addition to the 28 Americans missing, the ship also carried five Polish crew members.
“The debris is scattered about over several miles”, said Coast Guard Chief Petty Officer Ryan Doss, of the Miami station.
The Met Office predicts the United Kingdom is facing unsettled weather over the coming days with storm-force winds of around 50mph expected later next week.
“The ship was simply in the wrong place at the wrong time”, he added, saying Joaquin was just a tropical storm when El Faro set out but it intensified rapidly into a major hurricane. It later weakened to a Category 3 before regaining strength again on Saturday.
The US Coast Guard said the crew earlier reported it had been able to contain the flooding. They resumed their efforts at first light.
“There’s so much wind, thunderstorms and sea spray that it is hard to see”, Coast Guard Capt. Mark Fedor told CNN’s Eric Burnett.
The vessel carried 685 containers and had on board an EPIRB, which transmits distress signals.
Other agencies involved in the search include the US Air Force and the US Navy.
Police say they responded to 74 crashes and 52 disabled vehicles by midday Friday.
The find was reportedly made by the El Yunque and a tug boat hired by TOTE to look for their missing sister ship.
Hurricane warnings are in effect for the Central Bahamas, Northwestern Bahamas, and Southeastern Bahamas.
Friday, the storm destroyed houses, uprooted trees and unleashed heavy flooding across the Bahamas.
Emergency teams said there were no reports of casualties in the Bahamas. Officials have already reopened more than a dozen small airports across the island chain.
A weaker Hurricane Joaquin continued to move away from Bermuda on Monday morning and was expected to slowly lose steam over the open Atlantic.
This satellite image taken Friday, October 2, 2015 at 12:45 p.m. EDT, and released by the National Oceanic and Atmospheric Administration (NOAA), shows Hurricane Joaquin, bottom center, pounding the Bahamas and a deepening low pressure system on the US east coast.
The Bermuda Weather Service has issued a tropical storm warning and a hurricane watch for Bermuda.
The U.S. National Hurricane Center says Joaquin remains an “extremely dangerous” storm heading on a northeastward forecast path toward Bermuda.
Even with Hurricane Joaquin no longer as big of a threat, the weekend promises little relief for the most waterlogged parts of the East Coast. “It’s really a mess and we are going to have significantly more problems with multiple rivers reaching moderate flood (level) or higher”.
Eyewitness News Meteorologist T.J. Del Santo said regardless of the exact track of Joaquin, the coast of Southern New England will get large ocean waves, risky rip currents and beach erosion.
Swells generated by Joaquin will continue to affect portions of the Bahamas during the next few days.