Officials moved in after sewage samples from Block 9 of Richland Gardens and Hong Wing House of the Cheung Hong Estate came back positive for Covid, and authorities suspected there were asymptomatic patients.
The overnight testing operations are expected to end at 11.30am and 1pm on Sunday respectively.
Earlier, the government found 56 positive Covid cases after sealing off two buildings in Kowloon Bay and two other blocks in Chai Wan overnight, during which more than 2,700 people were tested.
In Chai Wan, thirty-four cases were found in Tsui Fuk House of the Tsui Wan Estate from around 1,150 residents who were tested.
Tsui Luk House of Tsui Lok Estate saw a dozen cases and 14 undetermined ones, after testing around 562 people.
A separate overnight operation at Blocks 5 and 6 of Richland Gardens in Kowloon Bay reported 10 positive cases and two indeterminate results from testing some 1,015 people.