Colombian President Juan Manuel Santos said the troops were needed “to assure normality”.
Clashes with police broke out after thousands of people took to the streets in support of the farmers. At least two people have died.
Farmers say government policies are driving them into bankruptcy.
“Last night, I ordered the militarization of Bogota and I will do the same today in any municipality or area that needs the presence of our soldiers,” Juan Manuel Santos said in a televised address after an overnight cabinet meeting.
“It’s unacceptable that the actions of a few impact the lives of the majority.”
He did not say how many troops would be called in.
President Juan Manuel Santos had earlier described the protests as “valid”, but urged demonstrators to keep them peaceful.
Clashes broke out on Thursday afternoon after tens of thousands of people marched peacefully in support of a 10-day protest by small-scale farmers.
Correspondents said masked youths threw stones and bricks and fought riot police who responded with tear gas and water cannon.
The two deaths occurred overnight in the western districts of Suba and Engativa, although the circumstances are not yet clear, Bogota security chief Alfonso Jaramillo said.
Interior Minister Fernando Carrillo said that those who had resorted to violence were “vandals, not farmers”.
The protests have united potato growers and milk producers with teachers, health workers and students – and negotiations with the government remain deadlocked.
Protesters in other parts of the country have also been blocking roads and disrupting food supplies to major cities and towns.
On Wednesday the government announced measures – including better prices for agricultural products and more access to loans – to ease the pressure on farmers.
The government also promised more protection from products imported at lower prices from countries with free-trade agreements with Colombia.
But the small-scale farmers have so far rejected the government’s offer.
They say that free trade agreements with the EU and the US, which have recently come into force, are flooding the market with agricultural products at prices they are unable to match.
They also complain that rising fuel and production costs have turned small-scale farming into a loss-making business.
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