Residents of Block C of New Kwai Fong Gardens and On Shun Building in Kwai Fong and Kwun Tong were ordered to undergo mandatory testing after one person from each building tested preliminary positive for Covid-19.
Blocks 1 and 2 of Hsin Kuang Centre in Wong Tai Sin were also locked down after sewage samples from the buildings tested positive for the virus.
An official said this indicated there might be asymptomatic patients living in the buildings.
The government said it aimed to complete the lockdown operations by Friday morning.
Anyone else who spent more than two hours in the buildings between January 21 and January 27 are also required to get tested for Covid before this Saturday, along with any person who had been in the Hsin Kuang Centre M2 Square shopping centre or its car park during that period.