It was the first time the virus was detected among poultry in the Czech Republic, said Zbynek Semerad, a spokesman for the Czech veterinary authority.
Of the 6,000 turkeys at the farm in Tisova, 100 kilometers (60 miles) east of Prague, 1,800 have died of the virus. The rest will be slaughtered.
The tests were conducted by a reference laboratory in the Czech Republic.
The illness has not been detected in any humans. The Czech news agency CTK reported that farm workers will receive the Tamiflu anti-viral drug as a precaution.
World health experts have been tracking the H5N1 strain of bird flu out of concern that it could mutate into a form easily transmittable between people and cause a flu pandemic.