The 59-year-old man allegedly has been molesting his daughter, who is now 35, since she was a child.
Arcedio Alvarez - dubbed "monster of Mariquita" by the local press - has been taken to jail under police and army protection and is being held in custody, news agency Reuters reported.
He denied rape and incest charges when he appeared in court in the central Colombian region of Tolima, saying his daughter was adopted.
"We agreed to have a romantic relationship because we really loved each other. But she was not my own child," the BBC reported he told the court.
The woman, Alba Nidia, told police the abuse started when she was nine. She'd been in her father's care since her mother died when she was five. She says she has given birth to 11 children, three of whom have died. The surviving children, reportedly aged between one and 19, are now in state care.
"I always respected him as my father and he is my father," she was quoted as saying on the BBC.
"He never spoke about (incest), about why we were doing it. Sometimes I would ask him and he would say it was God's will."
She said in an interview with the daily newspaper El Tiempo that a Christian pastor had convinced her to reveal the allegations.
"I took this decision according to the will of God, thanks to a pastor who prayed for me many times," she said in the interview. "That is what gave me the strength."
The case has prompted comparisons with the high-profile case of Austria's Josef Fritzl, who was recently convicted of holding his daughter captive for 24 years in the basement of his house and fathering her seven children.
Colombian media reported that the woman decided to file a complaint against her father when she saw television reports about Fritzl, news agency DPA reported.
"She started to reflect on the issue when she saw the case of the Austrian 'monster'. She realised that what her father was doing to her was not normal," a relative told reporters.
The woman said she decided to file suit after her father beat up two of her children, aged two and five.
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