It has kept infections under 10,000 with some 170 deaths by imposing effective but economically punishing social distancing measures for much of the last year.
Over the last two months the city has been hit by a fourth wave of infections with authorities struggling to bring the daily numbers down.
Stubborn clusters have emerged in low-income neighbourhoods notorious for some of the world's most cramped housing in the district of Yau Tsim Mong.
Thousands of Hong Kongers were ordered to stay in their homes on Saturday for the city's first coronavirus lockdown as authorities battle an outbreak in one of its poorest and most densely packed districts.
The order bans anyone inside multiple housing blocks within the neighbourhood of Jordan from leaving their apartment unless they can show a negative test.
Officials said they planned to test everyone inside the designated zone within 48 hours "in order to achieve the goal of zero cases in the district".
The South China Morning Post said the measures covered about 150 housing blocks and up to 9,000 people with hundreds of police on standby to enforce the lockdown.
Hong Kong was one of the first places to be struck by the coronavirus after it burst out of central China.