A protest by thousands of Colombian farmers and truckers, which has blocked roads nationwide and become increasingly violent, has been infiltrated by Marxist FARC rebels, Defense Minister Juan Carlos Pinzon said on Thursday.

Clashes between police and agricultural workers became violent this week as authorities sought to remove dozens of roadblocks that have snarled travel on Colombia's highways and prevented produce getting to market.

Rocks and explosives were thrown as police launched teargas to clear protesters that Pinzon said have been mobilized in some areas by the Revolutionary Armed Forces of Colombia, or FARC.

The demonstrations, which began on Monday, are the second wave of so-called national strikes against President Juan Manuel Santos' agriculture and economic policies which farmers say leave them unable to make any profit.

Much of the violence took place in central Boyaca province, a key farming area, as well as southwestern Cauca.

"Everyone knows that the terrorist FARC end up infiltrating these kinds of protests and cause disorder," Pinzon told reporters in Bogota.

"There are sectors that infiltrate these situations because, let's be frank, potato farmers, valuable people, workers, are not really prepared to use explosives against the police or burn cars; there has to be evil minds behind that."

Potato, corn and milk producers complain that free trade agreements with Europe and the United States have made it difficult to compete with cheap imports.

Some coffee growers have joined the protests, seeking more effort by the government to weaken the currency. They also want help to pay for fertilizers and other farming chemicals.

The FARC, which began as an agrarian struggle against rural inequality in 1964, on Monday issued a statement of support for the protest.

Pinzon's accusation against the FARC comes as the rebel group seeks to raise its influence in rural areas while it negotiates with the government on a peace deal to end its insurgency.

The two sides are currently discussing the rebels' inclusion in the political system if peace is achieved after reaching partial accord on agricultural reform.