Police urged them to stop for safety reasons and were investigating who was responsible.
Traffic authorities said several roads in the central and eastern Netherlands were completely or partially blocked by the early morning blockades and fire services rushed to clear roads as traffic built up.
Clean-up operations were expected to take hours on some roads.
By the end of the day, some roads were still not cleared, in part because some companies involved in the clean-up had received threats, said Diederik Fleuren, a spokesman for the the government's roads and waterways organisation Rijkswaterstaat.
"We are doing everything to clear the roads but... some contractors are being intimidated," Fleuren told the Associated Press in a telephone interview.
He said it was not clear when all the roads would be fully cleaned.
"It is very extreme now that people are being threatened" for assisting the clean-up, he added.
Dutch media reported that at one location, a sign was left behind that said: "Sorry for the inconvenience, Rutte IV is driving us to despair," a reference to Prime Minister Mark Rutte's coalition government.
Police and security authorities appealed to farmers to halt what they described as dangerous situations.
"Protesting is a fundamental right and as long as it stays within the limits of the law, a lot is possible," the emergency services said in a joint statement.
But they said the latest actions "seriously endanger road safety and can lead to life-threatening situations for road users".
The latest demonstrations came a day after a government-appointed mediator sent invitations to farmers' organisations to discuss with the country's ruling coalition ways of reducing nitrogen emissions.
"I see the talks as a turning point: breaking the deadlock together," mediator Johan Remkes said.
"The cabinet has assured me that there is room and joint solutions are possible."
But some farmers have rejected the appointment of Remkes as an independent mediator because he is a member of Prime Minister Mark Rutte's centre-right political party and a former deputy prime minister.
The farmers are angry at government targets for reining in emissions of nitrogen oxide and ammonia that they say threatens to wreck their agricultural way of life and put them out of business.
The government says emissions of nitrogen oxide and ammonia, which livestock produce, must be drastically reduced close to nature areas that are part of a network of protected habitats for endangered plants and wildlife stretching across the 27-member European Union.
The ruling coalition wants to cut emissions by 50 per cent across the country by 2030, calling the measure an "unavoidable transition" to improve soil, air and water quality in a EU country known for its intensive farming practices.
It has called on provincial authorities to draw up plans to reduce emissions and earmarked an extra 24.3 billion euros ($A35.5 billion) to fund the changes.
Farmers argue that they are being unfairly targeted while other industries, such as aviation, construction and transport, also are contributing to emissions and face less far-reaching rules.
They also say the government is not giving them a clear picture of their futures amid the proposed reforms.
