Humans rarely contract the bacterial sickness known as Q-fever, but the unusual outbreak in the Netherlands has been growing since 2007 and is believed to have infected 2,300 people this year.
The Agriculture Ministry ordered preventative measures, including vaccinations and a transport ban earlier this month, as well as the slaughter of pregnant animals. These carry the bacteria in high concentrations and are believed to be the main source of human infections, which usually occur during the goats' birthing season.
Agriculture Ministry spokesman Thijs van Son said culling had begun on three out of the 60 farms currently identified as having infected animals.
On infected farms, pregnant females were identified by echosonogram and marked with red paint, while others were marked with green paint.
Farmer Henk van Loon described how his milk goats were sedated, then killed with a lethal injection.
In all, 40,000 infected goats and sheep will be killed over the next month. Van Son said twice that many will likely be destroyed before the birthing season begins in March, as more cases are still being identified.
Though Q-fever usually causes only flulike symptoms in humans, it is known to present an extra threat for people with autoimmune diseases and with heart valve problems.
Experts believe the outbreak in the Netherlands, the most severe on record, is due to intensive farming combined with the country's dense human population.
There are about 1.2 million sheep and 400,000 goats on 350 farms in the Netherlands, a country of 16 million people.