"Avian influenza has been detected on a poultry farm at Zoeterwoude, where some 28,000 birds are affected," the economy ministry said in a statement.
"The birds are infected with the H5 variant of the flu but it's not yet known whether of the highly pathogenic variety or not," it added.
The highly-infectious H5N8 strain of bird flu was discovered in the Netherlands two weeks ago, where authorities suspect it might have been brought in by birds migrating from Asia.
Dutch authorities have said human infection can only occur following "intense and direct contact" with infected birds.
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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.
The latest outbreak lies about 35 kilometres (21 miles) northwest of Hekendorp, where the first outbreak was detected in mid-November, leading to around 150,000 birds being destroyed.
Authorities today were destroying the birds at the latest outbreak at Zoeterwoude and have thrown a 10-kilometre cordon around the farm.
Four other poultry farms in the area are being investigated for bird flu, authorities said.
The Netherlands' largest agricultural organisation, the LTO, said today the latest outbreak was a serious setback in the fight again bird flu in the country.
"The blow is so much harder as we were on the eve of easing the restrictions we implemented in the last two weeks," Eric Hubers, who chairs the LTO's poultry arm, said in a statement.
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.