A method of repairing a phase shift mask includes exposing upper and side surfaces of the phase shift pattern of the mask, selectively forming a passivation layer on the surfaces of the exposed phase shift patterns, and then cleaning the phase shift mask on which the passivation layers are formed. The repairing of the phase shift mask is carried out in the midst of a series of photolithographic exposure processes in which the phase shift mask is used to transfer an image to a photoresist layer or layers. After the photomask is cleaned, a determination is made as to whether the transmittance of the phase shift pattern is above a threshold value.