The move came after authorities yesterday identified bird flu at a poultry farm at Zoeterwoude outside The Hague, where 28,000 birds needed to be culled.
"There is another poultry farm within one kilometre (over half a mile) of the affected farm," the economics ministry said in a statement.
"Now that H5N8 has been confirmed, the birds on that farm will now be culled. There are around 50,000 birds."
Two other farms within a 10-kilometre radius have been given the all clear, and another farm is under investigation, the ministry said.
Some strains of avian influenza are fatal for chickens, and pose a health threat to humans, who can fall sick after handling infected poultry.
Dutch authorities have said human infection can only occur following "intense and direct contact" with infected birds.
The H5N1 strain of bird flu has killed more than 400 people, mainly in Southeast Asia, since first appearing in 2003. Another strain of bird flu, H7N9, has claimed more than 170 lives since emerging in 2013.
Bird flu has been detected in at least three other locations in the Netherlands. Germany and Britain have also reported similar strains of the virus.
The H7N7 strain of avian flu severely hit the Netherlands in 2003 with health authorities destroying some 30 million birds in an effort to quash an outbreak.
There are some 95 million chickens on Dutch poultry farms and egg exports totalled some 10.6 billion euros (USD 13.2 billion) in 2011, according to the latest Dutch statistics.
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