1. A defect inspection method, comprising: imaging with an image acquiring unit the same region of a sample in a plurality of image acquisition conditions and acquiring a plurality of images for the same region of the sample; processing with a defect candidate extracting unit the plurality of acquired images of the sample and extracting a defect candidate in each of the plurality of images; clipping with a partial image clipping unit a partial image including the extracted defect candidate and a neighboring image of the defect candidate from the plurality of acquired images based on position information of the extracted defect candidate; obtaining with a feature quantity calculating unit feature quantities of the defect candidates in the plurality of clipped partial images; associating with a defect candidate associating unit the defect candidates that have the same coordinates and are detected in conditions in which the image acquisition condition is different among the extracted defect candidate; extracting with a defect extracting unit defect from among the associated defect candidates based on multi-dimensional feature quantity space data of feature quantities of the associated defect candidates; and outputting with an output unit information of the extracted defect.