China's agriculture ministry said on Saturday that 9,830 ducks had died in a village outside the southern city of Guangzhou between September 5 and 13.
Samples were being tested for the H5N1 bird flu virus and a further 30,000 ducks had been culled by officials since the outbreak.
Yu Yedong, director of the Guangdong Animal Epidemic Prevention Centre, told the Standard, a Hong Kong newspaper, that the ducks had been vaccinated against the virus.
He added a first vaccination was only 65 percent effective and the birds needed a second to make it 90 percent effective. Yu told the paper he believed the birds were infected after the first vaccination.
Ho Pak-leung, an expert in infectious diseases at Hong Kong University, told the Standard there were fears the virus had now mutated.
Bird flu has so far infected at least 25 people in China, including 16 who later died.
China conducted a huge campaign last year to contain the disease, slaughtering tens of thousands of poultry and stepping up public education efforts.
H5N1 has killed 200 people and ravaged poultry flocks worldwide since 2003, according to the World Health Organisation.