A method for operating a three-dimensional object printer compensates for inoperative ejectors. The method identifies image data values associated with an inoperative ejector that stored in a memory with other image data values for a three-dimensional object to be printed by the three-dimensional object printer. The method replaces the image data values associated with the inoperative ejector with image data values associated with an operative ejector that correspond to a material that is different than a material ejected by the inoperative ejector and operates a plurality of ejectors with reference to the other image data values and the replaced image data values to enable the operative ejector to eject drops of the material that is different than the material ejected by the inoperative ejector into the three-dimensional object at positions where the inoperative ejector would have ejected material.