Coronavirus cases have been confirmed among residents of both Man Ying Building in Jordan, and Hang On Building in Sham Shui Po.
Residents were required to stay put in their homes as tests are arranged, unless they had already gotten tested since Saturday and have proof of a negative result.
Authorities expected to complete the operations by 7am on Tuesday so people can get to work.
Officials also went around to seven buildings around Man Ying Building, handing out free Covid test kits and face masks to residents in a new pilot scheme aimed at encouraging more people to get tested.
Many experts have questioned the effectiveness of the overnight lockdowns, with many operations yielding few coronavirus infections.
But lockdowns overnight on Sunday found a significantly higher rate of infection, with three preliminary positive cases uncovered at Wai Lee Building in Quarry Bay, leading to a partial evacuation at the block.