The anti-government demonstrations erupted on Thursday, when more than 250,000 marched in a national strike.
They started peacefully but clashes between protesters and police have since broken out, and there have been reports of vandalism and looting.
Mr Duque said troops would carry out joint patrols with police.
"We express the total and absolute rejection of all Colombians for the vandalism, for the terrorism, for the looting," Mr Duque told reporters on Saturday.
At least three people have died since the protests against corruption and possible austerity measures began.
A curfew was imposed in the capital, Bogotá, on Friday, but it did not deter protesters from returning to the streets a day later.
When protests resumed on Saturday, police used tear gas to disperse hundreds of people who had gathered near Bogotá's National Park, reports said.
Demonstrators also gathered outside of congress in Bolivar Plaza, near the presidential palace.
Separately, late on Friday, three police officers were killed in a bomb attack in the country's south-west.
It is not clear if the incident is connected to the protests. The area is notorious for drug trafficking and gang violence.
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