More than 500 tractors, many decked out with the Danish flag, drove past the government's offices and parliament in Copenhagen to the port. Another 400 staged a similar protest in the country's second city, Aarhus.
Prime Minister Frederiksen's government has acknowledged that its decision to cull more than 15 million minks had no legal basis for those not contaminated by the Covid-19 variant, infuriating breeders.
Denmark, a country of around 5.8 million people, has been the world's leading exporter of mink fur for several decades.
It sells pelts for around 670 million euros ($792 million) annually, and is the second-biggest producer worldwide, behind China.
The mutated version of the new coronavirus detected in Danish minks that raised concerns about the effectiveness of a future vaccine has likely been eradicated, the health ministry said Thursday.
“It is not fair what has happened to the breeders,” said Daniel, 19, a mink farm worker.
“The entire sector will now have to shut down,” he added.
Frederiksen has already issued an apology and the agriculture minister resigned on Wednesday, but the plan is still to complete the cull of the nation's entire mink stock.
Despite her apology, Prime Minister Mette Frederiksen has insisted the cull remains “non-negotiable”.
Her government is now preparing legislation to make it possible — by banning mink farming until January 1, 2022.