The Hong Kong government's announcement on Tuesday was met with outrage from pet owners and animal rights activists, with several online petitions urging authorities to reconsider.
It comes after a new cluster linked to the pet store Little Boss, where a 23-year-old employee was confirmed positive for the Delta variant on Monday. A customer who visited the store and interacted with the employee was also later tested positive.
After investigating the pet store, officials said Tuesday that 11 hamsters had been tested so far positive for Covid, raising concerns about the possibility of animal-to-human transmission.
Environmental samples taken at the store's warehouse, where other species of small animals are kept, also confirmed traces of coronavirus, officials said. The hamsters in the pet store were imported from the Netherlands in two batches - on 22 December and 7 January.
On Tuesday, authorities seized all the small animals in the store, including hamsters, rabbits, guinea pigs and chinchillas, to be tested and killed - regardless of the test result - citing a public health hazard.
All pet stores selling hamsters in the city have been ordered to hand over the animals for slaughter, with similar orders to anyone who bought a hamster up for Christmas, starting December 22nd.
Pictures Tuesday night show Covid control workers in hazmat suits in several pet stores, disinfecting the premises and bringing out large red plastic bags.
All animals taken from the store would be treated "humanely," authorities said.
Authorities also suspended imports of all small animals into the city and told all pet stores selling hamsters to stop operating immediately until all of their small animals have tested negative. Officials on Tuesday urged residents to "adopt good hygiene practices" with their pets, including avoiding kissing them.
More than 20,000 people have signed the largest online petition calling on the government not to kill the animals. Some social media users said many hamsters may have been purchased around the holiday as gifts for young children.
"Hamsters are our family, everyone please think rationally, do not give them up because of an incident," said Hamster Concern Society, a non-governmental organization in Hong Kong.
The Hong Kong Society for the Prevention of Cruelty to Animals (SPCA) said in a statement that it was "shocked and concerned" by the government's decision, which "did not take into account animal welfare and human-animal ties."
In a Facebook post on Wednesday, the hamster group said it had been flooded with questions and prayers from anxious pet owners. "My household hamster was not bought from a pet store, but my family is very worried and wants me to send it away," said one owner, according to the group. "But I do not want that, is there any way to test my hamster?
According to the US Centers for Disease Control and Prevention, Covid-19 cases have been documented in animals that have probably caught the virus from humans - however, there is far less evidence to suggest the possibility of transmission from animals to humans.
But authorities defended the killing, claiming it was in the public health and safety interest.
Hong Kong has adhered to a strict zero-Covid approach aimed at eradicating all cases internally while maintaining strict border controls, although increasingly transferable variants - first Delta and now Omicron - are making it more and more difficult.
Hong Kong is one of the few places that still adheres to this strategy in the hope of reopening its border with mainland China, which continues to lock in millions of people in an attempt to eradicate Covid.
A spokesman for the city's Department of Agriculture, Fisheries and Conservation (AFCD) said Tuesday that all hamsters would be killed regardless of their test result because the virus' incubation time means "negative test results do not necessarily mean the hamsters have not been infected."
He added that the government does not have the facilities or means to test more than a thousand hamsters every day, let alone isolate and quarantine all small animals in the city - so killing them was "a safe and feasible way to control the epidemic."
Testing and isolating pets and killing only those determined to be a threat, "could not completely control the epidemic and could cause loopholes," he added.
The Chinese mainland has also taken similar measures against pets during the pandemic.
Both cases went viral on Chinese social media, sparking widespread outrage and anger among pet owners and sympathizers - although some posters claimed that human life was more important to protect than animals.
The Hong Kong AFCD spokesman also pointed to European countries such as the Netherlands and Denmark, which had carried out similar mass killings due to concerns about Covid transfer.
In November 2020, Denmark said it found a mutated strain of coronavirus among its mink population, which had spread to humans. In response, the government announced the slaughter of 17 million mink to stop the spread.
The Danish Parliament ordered an investigation into whether the ministers had known that the legal framework was lacking, and the investigation was to be completed in April.
CNN's Wayne Chang, Lizzy Yee and Teele Rebane contributed to this report. Additional reporting from Reuters..