Health workers slaughtered around 100,000 hens at a poultry farm at Hekendorp outside Gouda while 90,000 chicks were culled at Witmarsum, in northern Friesland.
In both cases "a highly-contagious strain of the H5 variant" was suspected, the ministry said in a statement.
There were no other poultry farms within a one kilometre radius of the outbreaks, it added.
"Both farms were cleared to prevent further spread of the disease," the ministry said.
Seasonal bird flu has been detected at various farms around the Netherlands since October, blamed mainly on migratory birds.
Dutch Agriculture Minister Carola Schouten on October 23 imposed preventative indoor containment on all commercial poultry farms after two dead swans were discovered carrying the highly contagious H5N8 variety of bird flu.
The new measures come as the Netherlands also battles a second wave of COVID-19 which continued to infect around 6,000 people a day.
Earlier this month, Danish authorities ordered the culling of the country’s 17 million farmed minks, which are raised for their fur, after a mutated version of COVID-19 was found to have spread from the animals to humans. Denmark’s agriculture minister resigned over the order, which was initially ruled to be unlawful. However, the government has moved ahead with the plans, arguing that it could seek legal grounds for the culling retroactively.