A coating and developing treatment apparatus includes a substrate transfer mechanism; a defect inspection section; means for controlling transfer of a substrate; means for classifying a defect based on the state of the defect; means for storing a transfer route of the substrate by the substrate transfer mechanism when the substrate has been treated by treatment sections; and means for specifying, based on a kind of the defect classified by the defect classification means and the transfer route of the substrate stored in the storage means, a treatment section which is a cause of occurrence of the classified defect, and judging presence or absence of an abnormality of the specified treatment section, wherein the transfer control means controls the substrate transfer mechanism to transfer a substrate bypassing the treatment section which has been judged to be abnormal by the defective treatment specification means.