The farm in Libotenice, about 45 kilometres (28 miles) north of Prague, had a total of 188,000 hens before Christmas.
"The culling of hens from halls affected by bird flu is under way," State Veterinary Administration spokesman Petr Majer told AFP.
"The numbers show that this strain, the highly pathogenic H5N1, is very aggressive and kills hens in particular fast and on a mass scale," he added.
He said vets would also destroy over a million eggs from the farm.
The Czech Republic has registered 48 outbreaks of bird flu this year, the highest number in a calendar year in history.
The disease is currently plaguing Europe, with France reporting an outbreak in its foie gras producing Landes region last week.
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