Her comments came as a horrific video emerged showing the public execution of a 22-year-old woman accused of adultery, amid fears that recent gains for women are under threat as NATO troops leave and Kabul seeks peace with the Taliban.
Clinton, who was addressing a world conference on Afghanistan's future, said: "The United States believes strongly that no nation can achieve peace, stability and economic growth if half the population is not empowered."
The top diplomat said the way forward "must include fighting corruption, improving governance, strengthening the rule of law (and providing) access to economic opportunity for all Afghans, especially for women". "All citizens need to have the chance to benefit from and contribute to Afghanistan's progress. The United States will continue to stand strongly by the women of Afghanistan," she added.
But the execution video could renew concerns that Kabul is not doing enough to protect women, particularly from so-called honour killings, which were common during the Taliban regime that ruled from 1996-2001.
In the video, a woman named as Najiba is shot repeatedly in the back in front of a crowd of men in Qol village in Parwan province just north of the capital Kabul.
The woman was married to a member of a hardline Taliban militant group and was accused of adultery with a Taliban commander, Parwan provincial spokeswoman Roshna Khalid told AFP Sunday.
"Within one hour they decided that she was guilty and sentenced her to death. They shot her in front of villagers in her village, Qol," she said, adding that the execution took place late last month.
Following the shooting a villager handed the video over to the provincial government, saying the security forces were "preparing a big operation to find the culprits".
The Afghan government issued a statement Sunday saying it "strongly condemns this un-Islamic and inhuman action by those professional killers and has ordered the Parwan police to find the culprits and bring them to justice".
British Foreign Secretary William Hague said he was "shocked and disgusted" by the reports of the execution.
"Such deplorable actions underline the vital need for better protection of the rights of women and girls in Afghanistan," he said in a statement.
The Afghanistan Human Rights Commission also expressed outrage, with executive director Mohammad Musa Mahmodi saying: "We condemn any killings done without proper trial. It is un-Islamic and against any human rights values."
Washington says significant progress has been made on women's rights since the US-led invasion of 2001 toppled the Taliban, with the number of girls attending schools soaring and more women gaining employment.
According to figures provided by the US State Department, out of the eight million students enrolled in schools today, nearly 40 percent are girls. That contrasts sharply with 2002 when there were only 900,000 children in schools, virtually none of them girls.
The US says there are now 175,000 teachers in Afghanistan, about a third of them women, thanks to $316 million spent on education initiatives.
US officials said Clinton had raised the issue of women's rights with Afghan President Hamid Karzai during her brief visit to Kabul on Saturday, warning that they were a litmus test for the country's progress.
The Tokyo talks have raised pledges of $16 billion in civilian aid for the conflict-torn nation over the next four years.
Representatives from more than 80 nations and international organisations gathering in the Japanese capital later adopted the "Tokyo Declaration", pledging support and cash for Kabul.
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