Authorities blamed a FARC dissident group for the mass abduction, which occurred in the Cauca region of southwest Colombia, an epicenter of world coca production.
Officials said guerillas and members of the public confronted and overwhelmed security services who were trying to reestablish state control in two municipalities.
Government images showed gangs pelting a flaming armored vehicle with rocks, and riot police detonating smoke grenades amid a running gun battle.
President Gustavo Petro blamed a FARC renegade faction known as the Central General Staff (EMC), accusing it of "using the civilian population" to attack troops.
A statement from self-described "local communities," however, said locals acted in "self-defense" when attacked by the armed forces, who are alleged to have used machine guns and live rounds.
They expressed anger at government efforts to eradicate 8,000 hectares (about 20,000 acres) of coca in the area.
The statement also claimed that 28, rather than 29, security personnel -- including a police lieutenant colonel and army major -- were taken hostage as insurance against a new attack.
A local community organization released images of the captured security agents seated on plastic chairs in an open-sided pavilion, being served food.
Since October, Bogota has been trying to retake control of parts of Cauca from the EMC.
The group rejected a 2016 peace deal and has been raking in cash from drug trafficking, extortion, illegal mining and other illicit trades ever since.
- 'Total Peace' -
The kidnappings are an embarrassment -- and a stern challenge -- for Colombia's government, which is struggling with its worst unrest in a decade involving spasms of violence in several parts of the country.
"I demand their immediate release!" said Colombian police director Carlos Fernando Triana, vowing the police and military would remain in the area to "consolidate the rule of law."
The defense ministry accused the rebels of war crimes, saying they "not only forcibly recruit minors but also use and coerce the civilian population to drive out state forces" and prevent the state from providing access to "health, education, employment, and regional transformation."
The unrest is a direct challenge to Petro's signature policy of "total peace" by bringing all of Colombia's armed groups to the negotiating table.
Petro's critics say guerrillas, mafias and other armed groups have used the breathing room afforded them by the talks to expand their control over swaths of the country.
Much of the violence is driven by the fight over coca-growing areas and cocaine trafficking routes.
One faction of the EMC is in peace talks with the government but another faction withdrew from the negotiations last year and resumed attacks on state forces, which in turn stepped up operations against the group.
In a separate incident Friday, a Colombian soldier was killed and seven wounded in two attacks blamed on National Liberation Army (ELN) guerrillas in the Catatumbo region, a day after Petro visited the area which borders Venezuela.
The government has launched an ambitious economic development and coca eradication plan in the region, but insurgent attacks have left at least 76 people dead and 55,000 displaced since mid-January.
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