The government in the Muslim-majority country regularly bans books it considers threats to religious stability. "Allah, Liberty and Love" was banned in late May.
The website for author Irshad Manji says it is about "how to reconcile faith and freedom in a world seething with repressive dogmas."
Nik Raina Nik Abdul Aziz could face a two-year prison sentence and fine if convicted of the charge that was filed Tuesday.
Her lawyer Rosli Dahlan said the store was inspected before the book was banned.
Malaysia's Islamic courts have jurisdiction only over Muslims. A hearing was set for Sept. 19.
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