The book will not be included in the schools' curriculum, nor will it be stocked in school libraries, Mirza Kashif, president of All Pakistan Private Schools Federation, was quoted as saying by The Independent.
Malala attracted global attention last year when the Taliban shot her in the head in north-west Pakistan for criticising the group's interpretation of Islam, which limits girls' access to education. Her profile has risen since then, and she released a memoir in October, I Am Malala, co-written with British journalist Christina Lamb.
While Malala has become a hero to many for opposing the Taliban and standing up for girls' education, conspiracy theories have flourished in Pakistan that her shooting was staged to create an icon for the west to embrace.
Adeeb Javedani, president of the All Pakistan Private Schools Management Association, said his organisation had banned Malala's book from the libraries of its 40,000 affiliated schools and called on the government to bar it from school curriculums.
'Through this book, she became a tool in the hands of the western powers'
"Everything about Malala is now becoming clear," Javedani said. "To me, she is representing the west, not us."
Kashif Mirza, the chairman of the All Pakistan Private Schools Federation, said his group had also banned Malala's book in its affiliated schools.
Malala "was a role model for children, but this book has made her controversial," Mirza said. "Through this book, she became a tool in the hands of the western powers."
He said the book did not show enough respect for Islam because it mentioned the prophet Muhammad's name without using the abbreviation PBUH - "peace be upon him" - as is customary in many parts of the Muslim world. He also said it spoke favourably of the author Salman Rushdie, who angered many Muslims with his book The Satanic Verses, and Ahmadis, members of a minority sect who have been declared non-Muslims under Pakistani law.
In her book's reference to Rushdie, Malala says that her father sees The Satanic Verses as "offensive to Islam but believes strongly in the freedom of speech".
"First, let's read the book and then why not respond with our own book?" the book quotes her father as saying.
Malala mentions in the book that Pakistan's population of 180 million people includes more than 2 million Ahmadis, "who say they are Muslim though our government says they are not".
"Sadly those minority communities are often attacked," the book says, referring also to Pakistan's 2 million Christians.
The conspiracy theories around Malala reflect the level of influence that rightwing Islamists sympathetic to the Taliban have in Pakistan. They also reflect the poor state of education in Pakistan, where fewer than half the country's children ever complete a basic, primary education.
Millions of children attend private school throughout the country because of the poor state of the public system.
The Taliban blew up scores of schools and discouraged girls from getting an education when they took over the Swat Valley, where Malala lived, several years ago.
The army staged a large ground offensive in Swat in 2009 that pushed many militants out of the valley, but periodic attacks still occur. The mastermind of the attack on Malala, Mullah Fazlullah, was recently appointed the new head of the Pakistani Taliban after the former chief was killed in a US drone strike.
(With agency inputs)