Mohammad Karim, said to be aged around 60, was held in central Ghor province as he claimed her parents gave him the six-year-old girl as a "religious offering", officials said.
But officials cited the family of the girl — believed to be in shock — as saying that she was abducted from western Herat province, bordering Iran.
"This girl does not speak, but repeats only one thing: 'I am afraid of this man'," said head of the women affairs department in Ghor, Masoom Anwari.
The girl is currently in a woman's shelter in Ghor and her parents are on their way to the province to collect her, the local governor's office said.
"Karim has been jailed and our investigation is ongoing," the governor's spokesman, Abdul Hai Khatibi, said.
Child marriage 'fundamental breach' of rights
The arrest comes just days after a 14-year-old pregnant girl was burned to death in Ghor, in a case that caused shockwaves in Afghanistan.
The family of that girl, Zahra, said she was tortured and set alight by her husband's family.
But relatives of the teenager's husband insisted her death was by self-immolation.
The incidents underscore rising incidents of child marriages in Afghanistan.
"In some regions because of insecurity and poverty the families marry off their daughters at a very early age to get rid of them," Sima Samar, head of the Afghanistan Independent Human Rights Commission, told reporters this month.
Afghan civil law sets the legal age of marriage at 16 for girls, yet 15 per cent of Afghan women under 50 were married before their 15th birthdays and almost half were married before the age of 18, according to Save the Children.
"So many children who are married off at a young age are deprived of their right to education, safety and the ability to make choices about their future," the international charity said this month.
"This is such a fundamental breach of a child's basic rights."
The latest case comes after a young woman was stoned to death in Ghor last November after being accused of adultery.
And in March last year a woman named Farkhunda was savagely beaten and set ablaze in central Kabul after being falsely accused of burning a Koran.
The mob killing triggered angry nationwide protests and drew global attention to the endemic violence facing Afghan women.