Mawlawi Qalamuddin, the hard-line minister for the promotion of virtue and prevention of vice, who issued the decree, said the schools were functioning contrary to Islamic principles and that some outsiders were using them for launching anti-Taliban propaganda.
His ministry has also taken steps to stop Afghan female staff from working with United Nations agencies and non-government organisations. This latest move violates an agreement reached between the Taliban religious leadership and the United Nations last month promising talks on "problem areas", specifical ly access to education and health care for girls and women.
The Taliban now control four-fifths of the country and have imposed a series of draconian restrictions in Kabul since they captured the city almost two years ago, including education. Girls have been banned from all official schools and university and female teachers are no longer allowed to work in the capital.
However, the authorities have until now turned a blind eye to home-based schools where women trained as teachers under the previous communist regime but now officially banned from the classroom have been teaching basic reading, writing and numeracy skills for girls.
A senior Taliban official in the region, Hakim Mujahed denied that more than 100 such schools had been shut down following house-to-house raids by the religious police in Kabul. He said the move only affected a dozen illegal home-based schools.
"The problem is that the foreign agencies can't accept our strict rules and regulations," he said. "These schools were operating illegally and in secret moving to different locations every few days. This alerted us and made us very suspicious about their activities. They need to apply for permission and obey our laws if they want to reopen."
Observers believe that the current clampdown is a reaction to the way aid agencies have been circumventing the authorities' ban on women's employment. Foreign organisations allegedly have been passing off local female staff as health workers and paying salaries for some women teachers working in the unregistered home-based schools.
Aid workers fear that the ban in Kabul may lead to a clamp-down on home-based education elsewhere in the country.
They anticipate that this will lead to a further deterioration in the plight of girls and women, whose chances of surviving and leading healthy lives are already among the lowest in the world, according to basic development indicators.
A report published by UNICEF and the Save the Children Alliance earlier this month notes that one in four children dies before reaching the age of five, 50 per cent from preventable diseases. More mothers die in childbirth than in any other country and the literacy rate for women is the lowest in the world. Afghanistan ranks bottom of the 130 countries in the UNDP Gender Development Index.
A spokesperson for British aid agencies working in Afghanistan said: "Many agencies are very concerned at the continuing trend to deny women education and employment. If this ban is maintained the future for girls and women looks very bleak indeed - their very survival is under threat. People need to be convinced about the long-term benefits of educating their daughters."
Education has become a highly sensitive issue ever since the former Soviet-backed Communist regime tried to force families in highly conservative, rural areas to send girls to school. This bred resentment that continues to affect attitudes to education and women's rights today.