"An outbreak of a variant of H5 bird flu has been detected in a poultry farm in Zeeland province," Economic Affairs Minister Henk Kamp said.
All 42,000 egg-laying hens in the southern Netherlands farm will have to be culled "to stop the disease spreading" in accordance with European regulations, he added in a statement.
"A mild pathogenic variant of H5 can mutuate into a very contagious and deadly strain for chickens, therefore in all such cases the animals have to be put down."
It is a new blow for the Dutch poultry industry which since August has been at the centre of a tainted egg scandal that spread across several European countries and even as far as Hong Kong.
Millions of eggs were dumped, and some 3.2 million chickens were killed after the banned insecticide fipronil was found to have been used in poultry farms to combat lice, but had made its way into eggs.