The fate of more than 30 crew aboard a cargo ship missing off the Bahamas in heavy seas whipped up by Hurricane Joaquin was unknown on Friday as the storm battered the island chain for a second day.

News the vessel had lost contact with shore came as forecasters shifted the likely track of the potentially catastrophic storm further away from the US East Coast, but there were still warnings about the possibility of severe flooding in the Carolinas from unrelated heavy rains.

Late Friday afternoon, the US National Hurricane Center downgraded Joaquin, the third hurricane of the 2015 Atlantic season, to a Category 3 hurricane on a scale of 1 to 5, down from its previous Category 4 ranking.

By Friday evening, Joaquin's core was beginning to move away from the central Bahamas, the Miami-based center said in an 8pm EDT advisory, adding that hurricane conditions would continue for several more hours.

The storm, packing maximum sustained winds of 205 km per hour was about 40 km north-northeast of San Salvador in the Bahamas and moving northeast at 11 kph, the NHC said. The storm's movement was expected to gradually pick up speed in the next 48 hours.

The US Coast Guard said search and rescue crews were hunting for the 224 m El Faro and its 33 crew members after it was overcome by heavy weather from Joaquin off Crooked Island in the Bahamas on Thursday morning.

The ship, with 28 US citizens and five Polish nationals aboard, was headed to San Juan, Puerto Rico, from Jacksonville, Florida, when it reported it had lost propulsion and was listing and taking on water, the Coast Guard said.

The Coast Guard said there had been no further communications after the vessel issued the emergency call at about 7:30 a.m. Thursday.

The El Faro was in the eye of Joaquin about 56 km north of Crooked Island when it issued the distress call, according to Chief Ryan Doss with the Coast Guard in Miami.

"We have had 20-foot seas reported so it's going to take a while to get into the area," Doss said.

A Coast Guard cutter headed to help after taking part in a separate rescue mission off Haiti, while two Air Force Hurricane Hunter planes searched in vain for the U.S.-owned El Faro.

"The low cloud cover makes satellite communications difficult," Doss said, while the winds and high seas made it hard to get close enough by sea or air.

"The storm is so bad and slow moving it's hard for our planes to get low enough to inspect the surface of the water," he added.-Reuters