The authorities initially reported that 34 soldiers had been detained, but later revised the number to 33.
The mass detention of troops has become commonplace in southern Colombia.
According to the Government, such detentions are often carried out by residents who are manipulated by armed groups in areas where there is little state presence.
The clashes between the soldiers and armed rebels led by warlord Ivan Mordisco began on Monday (NZ time), leaving 10 dead.
The Defence Ministry said on social media that it had filed a complaint about the kidnapping to the public prosecutor’s office.
The army sent in “more troops to prevent any attacks in this hostile environment”, where the population “is being manipulated” by the rebels, a statement from military commander Admiral Francisco Cubides said.
Colombia has been enduring rising violence from dissident groups who reject a 2016 peace agreement between the Government and the bulk of the Revolutionary Armed Forces of Colombia (Farc) after a six-decade-long insurgency.
Last week, another group under Mordisco’s command detonated a truck bomb that killed six people and wounded more than 60 in the southwestern city of Cali.
- Agence France-Presse