The United Nations' Mission to Afghanistan (UNAMA) on Monday said three of its female Afghan employees had been temporarily detained by Taliban security agents and called on the group to stop intimidation of its local female staff.
Taliban spokesmen said they strongly rejected the allegations.
UNAMA said in a statement that the three women employed by the UN had been singled out by armed security agents and detained for questioning temporarily on Monday, but did not provide further details about the incident.
"The UN calls for an immediate end to all such acts of intimidation and harassment targeting its Afghan female staff, calling on the de facto authorities to reiterate and enforce explicit guarantees for the safety and security of all UN personnel operating in Afghanistan," the UN mission (UNAMA) said in a statement.
"There has been an emerging pattern of harassment of Afghan UN female staff by the de facto authorities," UNAMA said, referring to the Taliban administration.
Taliban deputy spokesman Bilal Karimi told Reuters the Taliban rejected allegations of harassment, saying the incident involved Propagation of Virtue and Prevention of Vice officials in the southern city of Kandahar.
"They wanted to know about a gathering of women, but then they realised that the gathering was related to UN female workers, they left them alone," he said.
Since the Taliban took over the country just over a year ago, no foreign capital has recognised the group's government and strict sanctions have isolated Afghanistan financially.
That has left many countries without an embassy in Kabul and caused the international community to cut development aid, leaving the United Nations and other NGOs to deliver hundreds of millions of dollars in humanitarian aid that is aimed at meeting urgent needs.
The group has placed growing restrictions on women's access to public life, closing girls' high schools in most provinces and saying women should cover their faces in public and not travel long distances without a male guardian.
Figures from international organisations show women's participation in the workforce has declined, though some women are still working outside the home.