Greek farmers have long-benefited from subsidies and tax breaks and have been shielded by successive governments in a nod to supporting agriculture and keeping an important voter base.
But their status as a protected group has come under threat as part of Greece's third bailout, prompting several protests in central and northern Greece.
On Wednesday, thousands of farmers rallied in central Syntagma square, waving the national flag and holding up banners which read "Hands off our land," Reuters reported.
Clashes erupted briefly when a group tried to break past a line of police in riot gear to reach parliament. Some protesters threw stun grenades and petrol bombs.
"We want to keep our land and to work and live in dignity," said Antonis Bitsakis, a farmer from the island of Crete, wearing a traditional black headband and holding a shepherd's crook. "We will fight to the end."
The government must present its agricultural development plan to its European Union and International Monetary Fund lenders by the end of the year.