The action is the first cull by the Netherlands authorities as bird flu sweeps through Northern Europe.
Outbreaks of avian flu, including the extremely contagious H1N1 strain, have been reported in Sweden, Finland, Denmark and Germany.
Dutch authorities have not confirmed which strain of the virus had been discovered at a poultry farm near Biddinghuizen, a village 70km (43 miles) east of Amsterdam.
The cull took place at four other sites run by the same company and a sixth farm less than one kilometre from the site of the original outbreak.
All farms in a three kilometre radius of the original outbreak are being checked for bird flu while a ban has been imposed on transporting poultry products within a radius of 10km.
The Netherlands is the world's second largest agricultural exporter and has more than 100 million hens, pigs, cows and sheep housed in high-intensity farms.
Such densely packed operations makes the animals more vulnerable to disease.
Since 1997, 40 million cows, hens, goats, pigs and sheep have been slaughtered to contain outbreaks of foot-and-mouth disease, swine flu and BSEReuse content