A defect repair apparatus includes a defect detection unit, a database, a defect repair unit, and a control unit. The defect detection unit inspects a multilayer substrate on which a repetitive pattern is formed and extracts positional information on a defect in the repetitive pattern and feature information on the defect. In the database, a plurality of defect repair techniques are registered. The defect repair unit repairs the defect of the multilayer substrate by a defect repair technique specified. The control unit reads a defect repair technique for the defect detected by the defect detection unit and controls the defect repair unit that repairs the defect by using the defect repair technique.