Gunmen stopped three night buses in Zabul province, on the main road between Kabul and the southern city of Kandahar, and kidnapped passengers, said provincial police chief Mirwais Noorzai.
He said he did not know how many people had been taken or their identity but the manager of a bus company and a provincial official said the gunmen had taken at least 14 Hazara people.
"The gunmen asked for identity documents and when people showed them, they took away only Hazaras," Sayed Mohebullah, a manager for the Ahmad Shah Abdali bus company, told Reuters.
He the gunman had also taken people from other buses. Asadullah Kakar, a member of the Zabul provincial council, said he believed 20 people, all but two of them Hazaras, had been taken away.
The Hazara are a Persian-speaking, mainly Shiite minority who have long faced persecution in Afghanistan, with thousands massacred by the Taliban and al Qaeda in the 1990s, but a series of murders and kidnappings this year has stoked a mood of growing despair.
Militants killed seven Hazara people, including women and children, in Zabul early this month and dumped their partially beheaded bodies.
The murders fuelled a growing sense of insecurity since the Taliban briefly seized control of the key northern city of Kunduz in late September and heightened the risk of sectarian hatred further poisoning relations in the ethnically diverse country.
No militant faction claimed responsibility.
Thousands of angry Hazaras took to the streets of Kabul on Nov. 11 to demand government action and justice for the seven. The protesters attempted to scale the walls of the presidential palace before police dispersed them with warning shots.
Seven people were wounded.