The buildings are located on 9-27 Pitt Street and 3 Tung On Street.
The lockdown order began at 7pm and the government aims to finish the operation by 6am on Wednesday, so residents can go to work.
The government said the buildings are within a “restricted area” that reported dozens of infections earlier. A spokesman also said many of the buildings here are dilapidated and feature sub-divided flats.
This follows a government operation last weekend that saw an area in Jordan locked down for about two days. More than 7,000 people were tested with 13 testing positive for the virus.
Earlier on Tuesday, Chief Executive Carrie Lam said future lockdowns would be smaller in scale and not be announced beforehand to prevent residents from fleeing.