The city's Agriculture, Fisheries and Conservation Department said it would offer a one-off payment of up to HK$30,000 (US$3,850) to shops affected by the culling of all hamsters on sale and tracing of people who had recently purchased them. They also banned imports.
"All these measures have affected the business of local pet shops selling hamsters," the department said in an announcement, adding that payments would be made from the government's anti-epidemic relief fund.
Last week, Hong Kong authorities enraged pet lovers with an order to cull more than 2,200 hamsters after tracing an outbreak to a worker in a shop where 11 hamsters tested positive.
People who had in recent weeks bought hamsters - popular apartment pets in the congested city - were ordered to surrender them for testing and what the government described as "humane dispatch".
In recent days thousands of people have offered to adopt unwanted hamsters amid a public outcry against the government and its pandemic advisers, which the office of Hong Kong leader Carrie Lam called irrational.
The link between hamsters and human transmission remains inconclusive, but government officials have said the crackdown was still needed as a precautionary measure.
Hong Kong has for months pursued a "zero-Covid" strategy, making it one of the most isolated major cities anywhere, with flights reduced by 90 per cent.
It is currently grappling with an Omicron outbreak however, with the government on Thursday announcng that it would extend citywide restrictions until Feb. 17.
Schools, playgrounds, gyms and most venues are shut, while tens of thousands of people must do daily coronavirus tests.
(Reporting By Greg Torode and Marius Zaharia; Editing by Angus MacSwan)