In an inkjet printer, a method for of compensating for defects in printed images identifies a cross-process direction location of a defect in a printed image and a candidate inkjet corresponding to the location of the defect. The method modifies the operation of the candidate inkjet to form a second ink image. The method identifies a second inkjet that actually formed the first image defect in response to identifying a second defect in the second ink image located proximate to the first defect. The method enables identification and compensation of inoperable inkjets when image data do not correspond perfectly to inkjets in the printer.