Sustained winds of up to 130mph were reported in parts of the eastern Bahamas, the US National Hurricane Center said.
The NHC says Hurricane Joaquin could affect the US East Coast by October 4, and said it was now an “extremely dangerous” storm.
Emergency teams said there were no reports of casualties in the Bahamas.
Forecasters in the US and the Bahamas are warning that central islands, many of which are low-lying, could see a storm surge of up to 12ft.
“We do not know the impact of 130mph on those areas,” Bahamas PM Perry Christie said.
“We know it’s a horrific kind of experience.”
Images on social media showed water reaching close to the roofs of some homes. The Tribune 242 website said dozens of people were trapped in their homes in the southern Bahamas.
After being classified only as a storm on September 30, Joaquin had become a Category Four hurricane – on a scale of five – by October 1.
The NHC said the storm could strengthen again as it nears the central Bahamas, but it is likely to lose strength as it moves north.
States along the eastern US coast – many of whom have suffered heavy rains in recent days – have warned residents to take precautions.
But the NHC, while warning the path of the hurricane could change, said it was “becoming optimistic that the Carolinas and the mid-Atlantic states will avoid the direct effects from Joaquin”.
Meanwhile, the governors of New Jersey, Virginia, Maryland and North and South Carolina declared states of emergency. One person was killed by flash floods in Spartanburg, South Carolina and schools in Charleston will be closed on October 2, local media reported.
Cuba has also issued warnings for four eastern provinces.
A White House spokesman said the Federal Emergency Management Agency (FEMA) was following the progress of Hurricane Joaquin and preparing in case it made landfall in the US.
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