The farm groups have said that they will continue strike action until Wednesday.
Official news agency Telam reported that federal Judge Guillermo Quadrini gave the order to clear the road of the protesters on Saturday.
"I believe they arrested us for blocking the road but nobody read us any charges," Juan Maya, one of those detained, told Maxima radio.
The protests, which have gone on for three months, were sparked by a decision by Cristina Kirchner, the president, to raise export taxes on grains by more than 10 per cent.
Roberto Fernandez, head of the Tramway and Motorised Drivers Union, said on Saturday that there would be a "total halt of activities" because of the lack of an agreement between the government and farmers.
There was no immediate reaction from the government, which has said that farmers' profits should be distributed to the benefit of poor Argentines.
Farmers say the taxes will make it difficult for them to reinvest any profits to continue making a living.
Protests and road blockades have led to shortages of goods like meat, oil, flour, vegetables and fuel, but Kirchner has said she will not abandon the tax increase.