According to the prosecution, the priest led a church in Los Pinos, a neighborhood in the affluent Las Americas district in the west of the city.
He was arrested on Saturday and surrendered to prosecution officials who will proceed with the trial.
The latest case of alleged child abuse by clerics adds to the “four or five” existing cases of alleged sexual abuse by priests, according to Colombia’s Catholic Church itself.
Secular entities have not made any pronunciations over the prevalence of sexual abuse of minors.
The Catholic Church that globally has faced a wave of criticism over the acts of pedophilia by clerics and the subsequent intended cover-up of many by church authorities.
According to the church itself, it is globally investigating 4,000 priests accused of sexually abusing children.
The church is facing 3,000 lawsuits over alleged sexual abuse in the United States alone, indicating that sexual abuse in the religious institution could be far more prevalent than the church has admitted.
Pope Francis, the highest official of the global Catholic Church, has deemed pedophilia a “leprosy” threatening the very foundation of the church. According to the pope, approximately one in every 50 priests could be guilty of the sexual abuse of children.