The government on Monday locked down two buildings, in Kwai Chung and Tin Shui Wai, after sewage samples there were found to contain the coronavirus.
Residents of Hei Lai House at Wah Lai Estate and Shui Fung House at Tin Shui (II) Estate were required to get tested.
The operations were expected to end at noon on Tuesday.
Meanwhile, health officials found 25 preliminary positive Covid cases after locking down a housing block in Ap Lei Chau.
Around 1,400 residents of Tung Yat House at Lei Tung Estate were tested, with five of the results indeterminate.