"According to the decision of the (Taliban) government, higher education for young women is prohibited until further notice," the decree states.
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The order stresses that it should be implemented as soon as possible and the ministry should be informed of the measures taken.
The Taliban had already been criticized for banning secondary education for girls.
The UN Assistance Mission in Afghanistan (Unama) has called on the authorities to allow girls to attend secondary school and expressed concern that if the ban remains in place, it will exacerbate the country's crisis and poverty.
Afghanistan remains mired in a deep crisis after two decades of armed conflict between the Taliban and governments that relied on military support from the United States and other North Atlantic Treaty Organization (NATO) countries.
The UN resident coordinator in Afghanistan, Ramiz Alakbarov, denounced in mid-August the growing marginalization of women after the return of the Taliban to power, as a significant setback in the economic, political and social rights of women was observed.
According to the diplomat, the full reintegration of women into the workforce is essential to transform Afghanistan's economy.