The country's veterinary authority spokesman Josef Duben said that 60 chickens tested positive at a farm in Norin, 140 kilometers (87 miles) east of Prague. He said further tests will be conducted to determine whether the birds have the deadly H5N1 strain.
All the 27,800 chickens at the farm, as well as poultry bred by local smallholders, will be slaughtered, Duben said.
The farm is just 4 kilometers (2.5 miles) from a turkey farm where an outbreak of the H5N1 strain was detected a week ago.
Last year, the H5N1 strain was found in 14 birds - all wild swans - in the Czech Republic.