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Colombia’s farmers continue their strike with no signs of ending anytime soon, as food shortages hit the capital city of Bogota, where the government has had to call in the troops to maintain civil order.

Serious questions have begun to be asked about president’s Manul Santos ability to govern a country that is in open revolt.

For months the campesinos (farmers) have warned of strikes. But no one in the government took them seriously, nor the steps to prevent a crisis that is now crippling the country and the government seems unable to resolve.

Early this week, president Santos told the nation that the “country is under control”.  A few days later the protest escalated. Road closures and clashes between protests and police, resulted in chaos in nine departments (states).

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More: Photo gallery of Bogota riots

Thousands of farmers and state workers marched through Bogota and other cities on Thursday, banging pots and pans as they converged after 11 days of blocking roads across the nation to prevent trucks reaching markets.

The protesters were mostly peaceful with many dressed in typical farmer attire of woolen ponchos and brimmed hats.

Then hundreds of masked activists rushed Bogota’s main square and pelted shop and bank windows with rocks, smashed bus stops and clashed with riot police who fired tear gas to disperse them.

Santos had tried to ease tension earlier on Thursday, acknowledging that the agriculture sector had been “abandoned.” But he called for peaceful dissent while talks about possible solutions continued.

But the situation turned violent, causing havoc across the capital, leaving two dead and parts of the city in shambles.

The violence in Bogota escalated after police fired tear gas in downtown Bogota Thursday and a curfew imposed in three densely populated areas of the city to control outbreaks of violence and looting.

Facing losing total control, almost two weeks after the first protests started, Santos was forced to call in the military.

“Yesterday I ordered the militarization of Bogota and I will do the same in any region or zone where the presence of soldiers is necessary,” Santos said after an overnight cabinet meeting, adding that he was making ready as many as 50,000 troops.

“There is no protest, as fair as it may be, that justifies loss of life.” the conservative Santos said. “We won’t let these vandals get away with this … Patience has run out.”

Troops were posted on street corners in the south of the city on Friday morning, although patrols were not yet visible in other areas.

The military will deliver food supplies by air and road to cities that are running low because of the roadblocks, Santos said.

Food prices have shot up in some places due to shortages.

The protests began as a strike by farmers angry at agricultural and trade policies they say have left them impoverished, and then spread to other sectors. Bogota, a city of almost 8 million people, has not seen a large military presence for at least a decade, when drug traffickers sought to pressure the government with bomb attacks.

The protests are the fiercest challenge yet to Santos, who took office in 2010 vowing to cut poverty while continuing the free-market policies that have boosted foreign investment, especially in mining and oil.

Farmers complain that life has become harder in recent years because income from harvests has failed to cover costs of fertilizers and transportation.

Potato, corn and milk producers say free trade agreements with Europe and the United States have made it almost impossible to compete with cheaper imports.

A series of droughts followed by unusually heavy rains has also made farming conditions difficult in recent years.

Santos is already under pressure after taking a political gamble to open peace talks in Cuba with Marxist guerrillas of the Revolutionary Armed Forces of Colombia, or FARC.