Around 2,000 farmers from the island of Crete, most of them carrying their characteristic wooden canes, gathered in front of the agriculture ministry after arriving by ferries.
They began pelting riot police with tomatoes and other items, broke windows in the ministry and set fire to dustbins.
Police, who blocked their route, responded with teargas, and arrested four people.
"The first floor of the building sustained damage, it is fortunate that no staff were hurt," Agriculture Minister Evangelos Apostolou later told reporters.
Police also confronted other farmers from the Peloponnese peninsula who tried to break through barriers into the city centre from a western suburb with their farm vehicles.
The farmers are angry about government plans to increase their social security contributions as part of a wider reform of the country's ailing pension system. They also reject plans to double their income tax by 2017 and scrap benefits such as cheaper fuel.
The Cretans were to be joined later in the day by farmers from across the country for a mass rally in front of the parliament.
Since mid-January, farmers have used their tractors to block dozens of highways.
Earlier this month they also began blockading border crossings to Bulgaria and Turkey.
But following an appeal from Sofia on Tuesday, they allowed trucks to pass for several hours a day at one crossing into Bulgaria.
The farmers threatened to further escalate the protest by blocking ports and airports at the weekend.
Prime Minister Alexis Tsipras, whose options are limited after signing a new bailout with Greece's international creditors in August, offered the farmers a compromise on Wednesday.
"There is significant room for improvement on their social security contributions, on the issue of when the measures take effect, and generally over the need to protect their income," he said.
Greece's creditors the European Union and the IMF have insisted on the reforms as a condition for loans to the debt-ridden country.
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