The three countries would be classified as "extremely high risk" after there had been multiple imported cases carrying the strain into Hong Kong in the past 14 days, the government said.
People who have stayed in these three countries for more than two hours will also be banned from boarding planes to enter Hong Kong. The suspension will last 14 days.
The ban came as Hong Kong started implementing on April 14 the tightened commercial flight suspension mechanism and the place-specific flight suspension mechanism to address the risk of importing mutant strains of Covid-19 from high-risk places.
According to the mechanism, if a total of five or more passengers in all flights from the same place were confirmed by arrival tests for Covid-19 with the N501Y mutant strain within a seven-day period, any passenger flights from that place will be prohibited from landing in Hong Kong for 14 days.
The city reported 30 new coronavirus cases on Sunday, 29 of which were imported, marking the highest daily toll since March 15. Hong Kong has recorded 11,683 cases in total and 209 deaths.
Airlines impacted by Hong Kong's ban on travellers from India, Pakistan and the Philippines include carriers such as Cathay Pacific, Hong Kong Airlines, Vistara and Cebu Pacific. - China Daily/ANN