The Department of Animal Production and Health deployed 30 officers to isolate the poultry farm in Bingiriya, 80 kilometres (50 miles) north of the capital Colombo and destroy its animals, director general Kumar de Silva said.
A total of 6,000 birds were destroyed, local officials said.
"We have carried out extensive tests and confirmed that a few birds had H5N2 strain of flu which is not the virulent H5N1 bird flu," de Silva told AFP. "We decided to destroy the animals as a precautionary measure."
He said local scientists feared that the milder form of the virus could mutate.
There have been no cases of H5N1 detected in Sri Lanka, de Silva said. Read More