The sentence for married adulterers, along with flogging for unmarried offenders, appears in a draft revision of the country's penal code being drawn up by the ministry of justice.
It is the latest in a string of encroachments on hard-won rights for women, after parliament quietly cut the number of seats set aside for women on provincial councils, and drew up a criminal code whose provisions will make it almost impossible to convict anyone for domestic violence.
Activists fear that as western troops head home, taking with them both money and the attention of the voting public back home, conservatives are making headway in undermining rights they see as a foreign imposition.
"It is absolutely shocking that 12 years after the fall of the Taliban government the Karzai administration might bring back stoning as a punishment," said Brad Adams, Asia director at Human Rights Watch. "President Karzai needs to demonstrate at least a basic commitment to human rights and reject this proposal out of hand."
A translated section of the draft seen by the Guardian has several references to stoning, including detailed notes on judicial requirements for handing down the sentence.
"Men and women who commit adultery shall be punished based on the circumstances to one of the following punishments: lashing, stoning [to death]," article 21 states. The draft goes on to specify that the stoning should be public, in article 23.
A working group including officials from the UK and US embassies, the United Nations and other international bodies is supervising the slow process of trying to unify a fragmented penal code, which has already dragged on for over a year, a source connected to the process said.
The provision on stoning was drawn up by a sub-committee working on sharia law, and has not yet been put to the main working group for approval. But its inclusion even in the draft is a warning sign that conservative judges and lawmakers are feeling bolder, women's rights campaigners said.
Although current sharia provisions make reference to physical punishments, or hudud, mandated under Islamic law, they do not specifically mention stoning, said Wazhma Frogh, executive director of the Research Institute for Women, Peace & Security.
"In the whole history of Afghan law we never had an official punishment of stoning … we are very worried about the return of the Taliban-like treatment of women."
It will be hard to campaign against the sentence being enshrined in national law now though, she warned, because critics in the conservative nation would leap to accuse them of defying Islam.
"It has been a punishment under sharia, so its almost impossible for many of us to take a public position [against it]," she said. "We as women's organisations have to come together, but at the same time it's very scary."
Although stoning is on the penal code of neighbouring Iran, it has been banned in many Muslim-majority countries including Morocco, Algeria and Indonesia.
And when a video surfaced a year ago of a young woman being stoned to death in an insurgent-controlled village a few dozen miles from Kabul, it was strongly condemned by government officials as well as rights groups and diplomats.
A senior official at the ministry of justice confirmed there was a provision for stoning in the sharia provisions of the draft penal code, but said the cautious drafting process was barely half complete.
"40% or 50% of this code is complete," said Dr Abdul Raouf Herawi, head of the department for new legislation. He said the evidence standards for stoning offered rigorous protection.
"Stoning is very sensitive in Islam, there are a lot of conditions … for example there must be four eyewitnesses who are absolutely sure, if just one is even a little unsure then it won't go ahead."
When the draft is complete, and approved by the working committee, it will be reviewed by the ministry before going to the presidential palace and then finally to parliament for approval.
EUPOL, the European Union police mission that chairs the Criminal Law Reform Working Group, said the "restoring of sharia law" had not been discussed on any committee its representative sat on.
The US embassy declined to comment, the UN did not respond to requests for comment and the UK embassy said it would "continue to work with the Afghan government to carry out legal reform in a way that is compliant with international human rights standards".