The closures "will have a devastating impact on the welfare of many of the city's neediest people, particularly women and children", the UN said in a statement released in Pakistan.
The Taliban also announced that it was closing many small, home-based vocational training programmes. Most of these have been run by international aid groups, which teach girls and young women to weave carpets and sew.
Under the new rules, however, schools will not be allowed to instruct girls older than eight and will be limited to teaching the Koran.
The schools on the closure list have violated those rules, the government said. "These schools weren't just for children. They also included 14 and 15-year-old girls," said the religious affairs minister, Haji Khulimuddin.
The home-based schools have mainly been run by women teachers who were forced out of work after the Taliban took control of Kabul in 1996 and imposed its harsh brand of Islamic law, banning women from the workplace and girls from schools.
Without officially recognising the home-based programmes, the Taliban has allowed them to operate until now.
A survey by aid workers in January showed that at least 107 home schools were operating in Kabul, teaching 6,500 students, half of whom were girls. They were teaching religion, language and maths.
The UN warned the Taliban that the decision to close the girls schools violated an agreement signed last month promising to discuss education and healthcare for women and girls.
The same agreement also promised to establish a joint committee "to discuss a range of humanitarian and development issues including problem areas such as access to education and health".
The Taliban's opponents, led by Afghanistan's former president Burhanuddin Rabbani and his military chief Ahmed Shah Massood, said that the Taliban's brand of Islamic interpretation was rooted more in tribal tradition than the Koran.