Initial reports said the woman was stoned to death, based on the decision of local religious leaders.
But a team from the Afghan Independent Human Rights Commission (AIHRC) says the woman, Amena, was beaten to death by her own family.
“The local religious leaders who, its seems, had a poor understanding of religious matters, issued a sentence ordering Amena to be killed," said Mohammad Farid Hamidi, a lawyer with the commission. "After the sentence was issued, Amena was handed to her paternal family, and [her family members] killed her. There was no stoning order. Based on our information, she was beaten to death."
The man in the case was publicly flogged, and then freed.
The Afghan government has launched an investigation into the killing.
“The Badakhshan police and security commander have sent us a report saying the women had an affair and that she was killed by her family members," Afghan Interior Ministry spokesman Lotfullah Mashal told RFE/RL's Afghan Service. "No stoning took place; it's a rumor; it isn't true."
The AIHRC's Hamidi said Amena's killing is a serious violation of both human rights principles and Afghan law. He said similar incidents of family honor killings have been reported in Afghanistan, although no reliable statistics are available.
More than five people have been arrested so far in connection with Amena's death. Hamidi said that more arrests are expected.
“The people who murdered Amena and also some of the people who issued the sentence [have been arrested]," Hamidi said. "We are calling on the Afghan government and on the judicial officials in the country to investigate this issue seriously so that such horrible human rights crimes are not repeated in the future.”
During the oppressive rule of the Taliban militia, women were regularly stoned to death for having allegedly engaged in extramarital sexual relations. Several stoning deaths were also reported in Badakhshan under the Afghan mujahedin in the 1990s. But there have been no known stoning deaths since the Taliban's ouster in late 2001.
Adultery remains illegal in Afghanistan. But Hamidi said that even if it was established beyond a doubt that Amena had committed adultery, she should have been tried in an official court.
“We can’t prove it was [adultery]," Hamidi said. "Proving adultery has its conditions and complications, and its own mechanism based on Afghan laws and Islam. So proving it is a key issue. Only after that can a punishment be considered and a sentence handed down."
Adultery is considered a grave sin under Islamic law, and punishment can range from flogging to death by stoning.
But proving adultery has taken place is not easy. The accused must make a confession and not retract it. It can also be proven through the testimony of four men, deemed trustworthy and pious, who witnessed the act.
The rights watchdog Amnesty International said Amena's killing demonstrates the failure of the Afghan government to dispense justice, particularly for women.
“We are absolutely appalled by this," said Nazia Hussein, an Afghanistan researcher with Amnesty International. "We think it is a grave violation of the fundamental rights of any individual. But it actually highlights discrimination against women in Afghanistan and particularly the customary practices which continue and are violating the fundamental rights of women across Afghanistan.”
In the last three years, the situation of Afghan girls and women has improved in terms of work and education. The new Afghan constitution -- adopted in January 2004 -- guarantees fundamental equality for men and women. But discrimination and violence against women are still widespread in Afghan society. Many victims remain silent due to social stigma, fear of persecution, or lack of legal protection.
Human Rights Watch researcher Zama Coursen Neff said the Afghan government should provide better protection for the country's women.
“We have seen that women in Afghanistan have very little protection from violence, whether it's violence by their family members, from their husbands, from their fathers; or whether it's violence from armed men who want to keep them from participating in public life in Afghanistan," Coursen Neff said. "We don’t know what’s happening in many places in Afghanistan because there are very few human rights monitors from the United Nations out there looking to see what’s happening, and things can happen to women with no one even knowing about it.”
The former United Nations rights expert on Afghanistan Cherif Bassiouni, after a visit to the country in February, called on Afghan authorities to do more to tackle violence against women.
(Afghan Service correspondents Farah Hiwad and Sultan Sarwar contributed to this report.)