Gen. Yasar Buyukanit was named in an indictment of three men charged with the bombing, the Los Angeles Times reported. Prosecutors say that two of the suspects are noncommissioned officers.
Ferhat Sarikaya, a prosecutor in the southeastern city of Van, charged that an illegal group allegedly formed by Buyukanit was behind the bombing. The bookstore was run by a Kurdish nationalist.
Buyukanit is in line to become chief of staff in a few months. He is a secularist, which places him at odds with the current Turkish government, run by former Islamists.
"Parts of this indictment went too far and had more political than legal content," the general staff command said in a statement.