The Coast Guard said the 224-metre ship named El Faro had taken on water and was listing at 15 degrees near Crooked Island, one of the islands most battered by the hurricane. Officials said the crew includes 31 US citizens and two from Poland.
"This vessel is disabled basically right near the eye of Hurricane Joaquin," said Capt Mark Fedor. "We're going to go and try and save lives. We're going to push it to the operational limits as far as we can."
Fedor said there were 20- to 30-foot (up to 9-meter) waves in the area, and that heavy winds could have destroyed the ship's communications equipment. The ship went missing when Joaquin was a Category 4 storm. The hurricane has since lost strength and become a Category 3 storm.
Messages left with Florida-based TOTE Services, the ship's owner, were not returned. The company said in a brief statement that it was working with the US Coast Guard and trying to establish communication with the ship.
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But the slow-moving storm continued to batter parts of the Bahamas, cutting communication to several islands, most of them lightly populated. There had been no reports of fatalities or injuries, said Capt Stephen Russell, the director of the Bahamas National Emergency Management Agency.
Officials were investigating reports of shelters being damaged and flooded, as well as two boats with a total of five people that remained missing.