The national avian influenza laboratory tested samples and confirmed the presence of the H5N1 avian influenza virus, stemming from an outbreak that began on July 14 near the town of Aksu, the agriculture ministry said.
A total of 3,045 chickens died in the outbreak, and agriculture workers culled another 356,976 birds to prevent the spread of the virus.
Agriculture and health officials set up emergency vaccination and quarantine procedures and had controlled the outbreak in the affected area of Aksu, the ministry said in a brief statement posted on its website.
China has reported dozens of cases of H5N1 bird flu in wild birds and poultry in the last two years. The last reported outbreak was in the northwestern region of Ningxia last month.
It has recorded 19 human infections and 12 deaths from H5N1 bird flu in China, though some experts believe that many more cases may have gone undetected.
The World Health Organisation (WHO) has asked for an investigation of a claim last month by Chinese scientists that China's first human infection with bird flu may have appeared in November 2003, two years before the government reported any cases.
The WHO had recorded 231 human infections with bird flu worldwide, including 133 deaths, by July 20.