"At the moment we know it is H5, but in all probability it will be confirmed as H5N1 as well. We expect the results tomorrow," Josef Duben said.
The two farms, one of 50,000 chickens and the second of 17,000, are within the three-kilometre (1.8-mile) exclusion zone thrown up around the village of Norin, where H5N1 was confirmed in a 28,000-strong flock of chickens at the end of June.
The Norin case followed a week after the Czech Republic's first case of H5N1 in domestic poultry was confirmed at a turkey farm at the nearby village of Tisova, where the remainder of a 6,000-flock was killed.
Czech authorities suspect bird flu initially spread to Norin on the shoes of a worker or on a car tyre between the two poultry farms, which belong to the same cooperative, ZOD Zalsi.
Since the initial Czech outbreak in June, other cases of the H5N1 strain of bird flu have been declared in France and Germany.