The two cases were near a chicken and turkey farm where the deadly strain of the virus was already confirmed at the end of June.
"All the birds will have to be killed within the three kilometre exclusion zone, including those of small breeders. Unfortunately, that is the way it is," Duben said. The liquidation is due to start Thursday.
The state veterinary service announced earlier Wednesday that H5 had been confirmed at the two flocks, totalling around 70,000 birds, which are mostly being raised for egg production, but the results of further tests were awaited to confirm the presence of the deadly H5N1 strain.
The two farms are within the three-kilometre (1.8-mile) exclusion zone thrown up around the village of Norin. The H5N1 strain was confirmed in a 28,000-strong flock of chickens there 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.
Since the initial Czech outbreak in June, other cases of the H5N1 strain of bird flu have been declared in France and Germany.