Prostitutes from mainland China were found in tiny "one-woman" brothels created from the toilets in a mostly vacant shopping mall in the outlying Yuen Long district, the South China Morning Post reported.
The cramped 14-square-metre blocks on the second floor of the building doubled up as the prostitutes' working and living space.
"I think it is the first time police have discovered public toilets turned into brothels," Chief Inspector Law Kwok-hoi said according to the daily.
There were a total of seven brothels, some converted from empty shops or office space, and operators dealt only with regular customers, who had to give a secret code before being allowed in, the newspaper said.
"An initial investigation showed up to 100 customers visited the seven brothels each day," Mr Law said, adding that each were charged HK$250 (1,060 baht) for sex services.
Police said in a statement that they had arrested 51 women and 35 men aged between 17 and 72 in the two day operation starting Tuesday, which included raids on more than 20 other locations.
Police seized a knife, metal pipes and a small amount of a drug suspected to be ketamine in the raids.
A quarter of those arrested in the raids which took place on Tuesday and Wednesday were suspected to have connections to triad gangs.
They were arrested for breach of conditions of stay, extortion, and possession of illegal drugs, among other charges.
The South China Morning Post report, citing police sources, said the brothels had been running for 10 months and that the raids were part of a nine-month operation into Yuen Long faction of the 14K triad society.
Prostitution is legal in Hong Kong, but soliciting and living off the earnings of prostitutes are criminal offences.
Hundreds of sex workers ply their trade in one-room brothels, saunas and bars throughout the city of seven million. Some operate independently but many, especially those from mainland China, are controlled by the city's notorious triads.