Yusuf Agar, the city’s deputy Mufti, said they should not have been placed among the books that were burned.
He said that happened by mistake, the Zaman daily reported.
Burning the books, that included a number of Quran interpretations, sparked anger in social media.
The city’s officials seem to have intended to burn books written by Fethullah Gulen, who is accused by the Turkish government of orchestrating an abortive coup last year.
Shortly after the attempted coup in mid-July 2016, Ankara blamed Gulen of masterminding and orchestrating the botched putsch, in which some 250 people lost their lives and about 2,200 sustained injuries.
However, Gulen, 76, who has lived in self-imposed exile in Saylorsburg, Pennsylvania, since 1999 and strongly opposes Ankara, denies any involvement in the coup attempt.