Michelle Bachelet gave no details of the killings in her speech to the Human Rights Council, but urged it to set up a mechanism to closely monitor Taliban actions.
Under a resolution agreed later on Tuesday by the Geneva forum, she is to report back at its September-October session on the situation and on any violations committed by the Taliban, and make a fuller written report in March 2022.
The Taliban treatment of women and girls would be "a fundamental red line", Bachelet told an emergency session of the council, held at the request of Pakistan and the Organisation of Islamic Cooperation (OIC).
Pakistan's ambassador Khalil Hashmi said the resolution voiced grave concern over reports of violations and sent a "message of solidarity to the people of Afghanistan".
Austria's ambassador, Elisabeth Tichy-Fisslberger, speaking on behalf of the European Union, said it was joining the consensus even though the resolution "falls short". The bloc had sought to launch an international investigation, she said.
Nasir Ahmad Andisha, a senior Afghan diplomat from the deposed government, called for accountability for Taliban actions, describing an "uncertain and dire" situation where millions of people fear for their lives.
"Monitoring is essential to prevent further atrocities and ensure accountability," Andisha told the talks.
Independent U.N. human rights experts, in a joint statement, said many people were in hiding as "the Taliban continues to search homes door-to-door" and property seizures and reprisals were being reported.
"The acts of the Taliban over the course of these months and to date may amount to war crimes and crimes against humanity," they said.
But China's ambassador to the U.N. in Geneva, Chen Xu, said that the U.S. Army and the militaries of other coalition partners, including Britain and Australia, should be held accountable for alleged rights violations by their forces in Afghanistan.
The United States condemned attacks that it said were being carried out against civilians, journalists, activists and minority groups, but did not name the Taliban.
Amnesty International said that its investigation into the massacre of nine ethnic Hazara men in Ghazni province last month was "proof that the Taliban's capacity for murder and torture has not diminished".
“The UN Human Rights Council special session has failed to deliver a credible response to the escalating human rights crisis in Afghanistan,” Agnes Callamard, Amnesty International's secretary general, said in a statement.