At an international forum in Islamabad, Khan hinted that keeping women away from education is a part of ethnic Pashtun culture.
Addressing the Organisation of Islamic Cooperation (OIC) meeting on Sunday, Khan seemed to offer the Taliban a pass when it came to limiting education for girls, urging the world to "understand" cultural differences.
Former Afghan president Hamid Karzai condemned Khan's speech and urged on Pakistan's premier not to speak on behalf of Afghans in such forums.
Former Afghan vice president Amrullah Saleh who lives in exile following the Taliban takeover, called Khan's remarks "disgusting and ignorant."
He said the comments indicated that Islamabad wanted Afghanistan to be uneducated and dependent on Pakistan.
Others on social media shared pictures of a father who used to walk her daughter's kilometres to school, as a response to counter Khan's narrative.
The Taliban, a predominantly Pashtun movement, issued a ban on girls returning to secondary school in Afghanistan after taking complete power in August.
The international community has repeatedly called on the Taliban to respect women and human rights in return for international recognition.
Pakistan's government is considered to be the main player in helping the Taliban to regain power after their defeat in 2001.
At the same conference, Khan urged the United States to "de-link" the Taliban regime from Afghan citizens to prevent a humanitarian crisis.
He said the Taliban had committed to complying with the pre-conditions for the lifting of economic sanctions.
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