This invention provides an examination method, an examination apparatus, and an examination program capable of performing the examination corresponding to the type or the like of the site to be examined and capable of reducing the examination time when examining the substrate. The X-ray is output from an X-ray source, and the X-ray that transmitted the substrate to be examined is photographed as an X-ray perspective image in an FPD (Flat Panel Detector). The photographing for generating the reconstruction data by X-ray CT is performed at the positions on the virtual circle having the optical axis of the X-ray source as an axis, similar to the photographing for generating the reconstruction data by tomosynthesis. Thus, in generating the reconstruction data by X-ray CT, the data is converted so that each image rotates using affine conversion with the center of each X-ray perspective image as an axis according to the rotation position on the virtual circle as if the X-ray perspective images obtained at the respective positions are photographed at the positions, and then the filtering process is performed.