Schoolgirls told the BBC they were devastated not to be returning. "Everything looks very dark," one said.
Taliban officials who seized power last month said they were working to reach a decision on the matter.
Many fear a return of the regime of the 1990s when the Taliban severely restricted girls' and women's rights.
Under their new government, Taliban officials have said that women will be allowed to study and work in accordance with the group's interpretation of Islamic religious law.
But working women have been told to stay at home until the security situation improves, and Taliban fighters have beaten women protesting against the all-male interim government.
On Friday, the Islamist group appeared to have shut down the women affairs ministry and replaced it with a department that once enforced strict religious doctrines.
'I am so worried about my future'
A statement issued ahead of Afghan schools reopening on Saturday said: "All male teachers and students should attend their educational institutions."
Secondary schools are usually for students aged between 13 and 18, and most are segregated.
Taliban spokesman Zabihullah Mujahid was later quoted by Afghanistan's Bakhtar News Agency as saying that girls' schools would open soon. He said officials were currently working on the "procedure" for this, and details including the division of teachers.
The spokesman told the BBC that officials were also trying to sort out transport for older schoolgirls.
Schoolgirls and their parents on Saturday said prospects were bleak.
"I am so worried about my future," said one Afghan schoolgirl, who had hoped to be a lawyer.
"Everything looks very dark. Every day I wake up and ask myself why I am alive? Should I stay at home and wait for someone to knock on the door and ask me to marry him? Is this the purpose of being a woman?"
Her father said: "My mother was illiterate, and my father constantly bullied her and called her an idiot. I didn't want my daughter to become like my mum."