The announcement noted that most imported COVID-19 infections could be detected by the coronavirus tests at the airport and in hotels.
The flight suspension rule had "little effect" on preventing imported infections and the risk of those cases causing infection in the community are "relatively minimal," the government said.
Travellers had griped that the regulation's last-minute flight cancellations also affected quarantine hotel bookings. Those impacted often had to postpone their rescheduled trips for weeks because hotels tend to be booked out months ahead.
Despite lifting the flight bans, travellers arriving in Hong Kong will still need to test negative for the coronavirus before arriving in the city, serve a mandatory quarantine period of seven days in a designated hotel in Hong Kong, and undergo a series of rapid tests and nucleic acid tests for the coronavirus over a two-week period.
Hong Kong leader John Lee and health authorities have said they are exploring options to keep Hong Kong open to international travellers, including a possible reduction of mandatory quarantine periods.