The paper considers the actual problem of debugging software critical information infrastructure systems. The paper offers an approach to the software quality assessment of CII systems, which defines the main stages of debugging and is based on applying models and methods within a multi-stage iterative process of obtaining programs of a given quality using generalized indicators. The generalized indicators composition will determine by the stages of debugging work during a multi-stage iterative process. Comparing groups of quality indicators of process sequence ensures efficient use of debugging techniques and tools.