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.
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 over 11,600 cases in total and 209 deaths.
Hong Kong authorities have been urging residents to get vaccinated for coronavirus with only around 9% of Hong Kong's 7.5 million residents vaccinated so far.
The government last week widened the city's vaccine scheme to include those aged between 16 to 29 years old for the first time, as they aim to boost lacklustre demand for inoculations amongst residents.