The ministry said Saturday that 9,830 ducks had died in a village outside the southern city of Guangzhou, not far from the border with Hong Kong, between September 5 and 13.
Hong Kong Health Secretary York Chow told reporters late Monday, citing the Chinese ministry, that the ducks had tested positive for the H5N1 strain of the virus.
Chow said the former British colony had immediately slapped a 21-day ban on imports of all live poultry, eggs and chilled or frozen meat from farms near the affected area on the mainland.
A ban on the import of such products from Guangdong province will remain in effect for a week, Chow said.
About 100,000 ducks were culled by local officials on Monday in a bid to keep the outbreak from spreading to other districts, Hong Kong media reported.
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.
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.
H5N1 has killed 200 people and ravaged poultry flocks worldwide since 2003, according to the World Health Organisation.
Scientists fear the virus could mutate into a form easily spread among humans, leading to a global pandemic with the potential to kill millions.