A method for compensating for inoperative ejectors in a three-dimensional object printer has been developed. A printer detects an inoperative ejector in a printhead. The printer identifies functional ejectors that print at locations adjacent to locations where the inoperative ejector fails to print a drop. The printer modifies firing signals for the functional ejectors so those ejectors print drops having an increased drop volume at the locations adjacent to locations where the inoperative ejector fails to print a drop. The printer prints a first layer of material drops using the modified firing signals. The printer advances the printhead in the cross-process direction between layers so that locations where the inoperative ejector fails do print a drop do not coincide between layers.