The All Pakistan Private Schools Federation will not allow the book, "I am Malala," to be read in the 152,00 schools the organization represents, The Independent reported.
The book will also not be allowed in the school's libraries.
The organization said the book would have a negative effect on students and that the book was not entirely respectful of Islam.
"Pakistan is an ideological country. That ideology is based on Islam. ... In this book are many comments that are contrary to our ideology," the federation's president, Mirza Kashif, said.
Malala's book received widespread international enthusiasm, but received mixed reviews in Pakistan, The Independent reported.
The government will not use the book in lessons at state schools but has not banned it.
Malala's book centers on her upbringing in Swat valley, her campaign for girls' education and the Taliban's attack.