Nik Raina Nik Abdul Aziz, who manages the bookstore chain outlet in the capital of Malaysia, Kuala Lumpur, is accused by the Islamic court of distributing Irshad Manji's "Allah, Liberty and Love."
The Home Ministry banned the book last month after it was deemed offensive to Islam, contained "elements that could mislead the public," and was "detrimental to public order".
According to Manji's website, the book "shows all of us how to reconcile faith and freedom in a world seething with repressive dogmas".
Nik Raina faces up to two years in jail and a fine if the Islamic court finds her guilty, her lawyer Rosli Dahlan said. No plea was recorded Tuesday with the next court date set for September 19.
Rosli said Islamic officials raided the store before the book ban was officially announced, and the shop had filed a court case to declare the raid illegal.
Rosli added that Nik Raina had no authority over deciding which books to sell and was being singled out because those in charge of merchandising were ethnic Chinese non-Muslims. Non-Muslims cannot be charged in Islamic courts.
Malaysia has a system of Islamic courts that run parallel to the country's civil courts and administer civil matters for Muslims who make up some 60 percent of the country's 28 million people.
Manji launched the book, together with a Malay-language translation, at a hastily arranged event in Kuala Lumpur on May 19 amid criticism by Muslims.
Her previous internationally acclaimed book, "The Trouble with Islam Today", is already banned in Malaysia. Malaysia frequently bans books, especially those deemed obscene or against Islamic teachings. But it is rare for Islamic courts to target bookstores.
New York-based Human Rights Watch has called on the government to reverse the book ban, saying it was "old-fashioned state repression" and "cowardly".