The slaughter of hundreds of goats on an intensive goat farm in Limburg was halted following a court order on Friday because test results for Q fever were inconclusive.
It is the first time a court has stopped the cull procedure, which covers all pregnant goats on farms where Q fever has been found.
The farm owner applied for an injunction to head off the cull after tests for the disease came up with conflicting results. He wants vets to take new samples and have them tested in different laboratories to find out if his herd really is carrying Q fever.
The judge will explain his ruling on Monday, news agency ANP reported.
In total, some 40,000 animals are to be killed nationwide in an effort to get the spread of the disease under control. Vets begin killing infected and pregnant goats towards the end of December.
The bacteria which leads to Q fever is released when infected sheep and goats have miscarriages and spreads easily.
By the end of November, some 2,300 people had developed Q fever and six had died, all of whom had other health problems.
Q fever was relatively unknown in humans prior to 2007 when factory farming of goats took off. The disease leads to flu-like symptoms in adults but can cause lung and heart problems.