The United Nations in Afghanistan warned of an "emerging pattern of harassment of Afghan UN female staff" on Monday.
The UNAMA mission said the three Afghan female employees were recently detained and questioned by local armed security agents.
The Taliban issued their own statement Monday evening, denying the women had been detained..
The Islamist officials said that local authorities had stopped a group of women in southern Kandahar province, but let them go after they learned they were working for the UN.
The UN also asked the Taliban to stop their intimidation tactics targeting its Afghan female staff, and reminded local authorities about their obligations under international law to guarantee their safety.
Islamists roll back rights for girls and women
The Taliban's strict interpretation of Islamic law has meant that women and girls have been severely limited in exercising rights like going to school or working.
The Taliban closed secondary schools for girls after taking power last year, and over the weekend, shut down secondary schools, or those with classes above sixth grade, that briefly reopened in Afghanistan's eastern Paktia province following a recommendation by tribal leaders.
The United Nations estimates that around 3 million girls have not been able to finish secondary school since the Taliban took power.
Afghan women call on UN to act
Meanwhile, Afghan women's rights activists told a UN Human Rights Council meeting in Geneva, which was held Monday, that they had virtually no rights in the country.
"Today, human rights in Afghanistan do not exist," women's rights activist Mahbouba Seraj told UN diplomats.
"Women of that country, we don't exist… We are erased," she told the Council.
"The women of Afghanistan are now left to the mercy of a group that is inherently anti-women and does not recognize women as human beings," said Afghan lawyer Razia Sayad.
Afghan women also urged the UN to set up a mechanism to investigate abuses in the country.
Richard Bennett, a human rights expert and the UN Special Rapporteur on human rights in Afghanistan, added that Afghanistan was facing a "descent towards authoritarianism" under its new rulers.
rm/dj (Reuters, AFP, AP)