Peng Cheng-yu (彭正宇), an official with the disease control center, said the carcasses have been identified as infected with the H5 strain of avian flu, a pathogenic virus that is causing global concern as a potential pandemic threat.
Farms inspected within three kilometers of the site were disinfected and cleared of any virus activity, Peng said.
According to the official, the dead birds were found abandoned near a stream in the county's Xinfeng Township by members of the public earlier this week, who then reported the incident to authorities.
The county's Environmental Protection Bureau has teamed up with the local police to determine from which farm the birds originated to ensure that other poultry have not been compromised, he said.
Those found guilty of endangering public health by abandoning animals or failing to report large numbers of potentially infected animals may face penalties of up to NT$1 million (US$32,500) under the Statute for Prevention and Control of Infectious Animal Disease, Peng warned.
According to Bureau of Animal and Plant Health Inspection and Quarantine (BAPHIQ) statistics, two poultry farms in Taiwan have been infected with avian flu so far this year, during which 11,271 birds have been culled.