The incident happened in the Ashkamish district of Takhar province.
The victim, who is in her 20s, told the BBC that she did not know the reason for the attack.
Although such mutilation is rare in Afghanistan, reports of violence against women are increasing.
The woman is now in hospital in Kunduz.
Her brother confirmed the nature of the injuries to the BBC, saying his aunt had seen the results of the mutilation.
A doctor at the clinic said the victim was six months pregnant, but lost the baby as a result of the violence.