Voluntary mass testing is carried out with the help of a medical corps of mainland Chinese workers.
A fitness workers’ union criticized the effort as a waste of resources, while activists said it could be used to collect DNA samples.
The government brazened the complaint as a smear campaign.
Hong Kong has so far controlled to keep the virus low with just under 5,000 infections shown.
But there are fears that several smaller waves could lead to a larger epidemic that is currently out of control.
The government hopes that the universal control effort will give an accurate picture of the spread and involve the pandemic.
Testing began Tuesday with more than half a million people registered to date. Hong Kong has a population of about 7. 5 million.
Health collects samples from more than 140 meeting centers across the city.
China has already tested the entire population of Wuhan, the city that experienced the first and worst epidemic in China.
A union of fitness workers criticized the project, saying that mass testing is an effective way to combat the pandemic.
The 20,000-member Hospital Employees Alliance said targeting would be a much better way to use resources.
Union leader Winnie Yu asked others not to participate and told reporters that major tests were necessarily being conducted to please Beijing.
“They will do everything they can to please China’s central government, even if it puts politics above all, ” he said.
Health experts are also involved that faulty tests can simply eliminate false negatives and that up to five million more people would want to get tested to end the third wave of existing infections.
A procedure to crack the government’s complaint in Hong Kong undermines the acceptance of the authorities.
Some activists expressed fear that samples will be used to gather residents’ knowledge and DNA.
Prominent pro-democracy activist Joshua Wong also suggested others boycott voluntary testing.
He said it “further fuels considerations that the plan is a large-scale DNA collection,” creating a path for a “China surveillance regime. “
Tensions are high between the teams for democracy in Hong Kong and the Chinese government after Beijing imposed a new national security law on the territory in June.
The law, which has been widely criticized internationally, allows life imprisonment for those China believes have committed acts of secession, subversion, and collusion with foreign forces.