Benitez Gilberto Zarate, 42, had fled in the wake of the accusation against him. But he denied any wrongdoing to police and local media, and has demanded a DNA test on the unborn child to back up his claim.
An international rights group is pressing the Paraguayan government to allow an abortion for the girl -- a procedure that health officials in the South American country have so far blocked.
At issue is Paraguayan law, which bans abortions except in cases where the pregnancy endangers the mother's life. The Paraguayan Ministry of Health says there's no indication that the health of the girl, now 22 weeks' pregnant, is at risk.
But the girl's family is asking for an abortion, and Amnesty International is backing the family. The group says her age should trigger the health exception and argues that pregnancy poses health risks to young girls whose bodies aren't fully developed.
Amnesty also says the law is too restrictive, noting that it doesn't provide additional exceptions for rape.
"The physical and psychological impact of forcing this young girl to continue with an unwanted pregnancy is tantamount to torture," Amnesty International official Guadalupe Marengo said this week. "The Paraguayan authorities cannot sit idly by while this young rape survivor is forced to endure more agony and torment."
Doctors learned the girl was pregnant after she entered a hospital in the Paraguayan capital, Asuncion, on April 21 for abdominal pain. That spurred a criminal investigation.
Authorities allege that she was raped by her stepfather, and that the pregnancy stems from that crime, according to the prosecutor in charge of the case, Monalisa Munoz.
The girl's mother has also been arrested in connection with the case, Munoz said. She faces charges including breaching her duty of care, Amnesty International said.
Amnesty said the girl's mother has also asked that her daughter be allowed to have an abortion. But Paraguayan Health Minister Antonio Barrios said the pregnancy would continue.
The girl, who has been transferred from a children's hospital to Asuncion's Red Cross Hospital, will be taken to a shelter where the state will oversee her prenatal care.
"The Justice Department will determine later who will have custody of the mother and child after (the birth)," Barrios said.
A 2013 United Nations report
said that 2 million girls under age 14 give birth in developing countries every year, many of whom suffer resulting long-term or fatal health problems. It estimated that 70,000 adolescents die each year from complications from pregnancy or childbirth.