The problem of the quality of automated systems can be solved both from a common standpoint and from the standpoint of ensuring the quality of individual system components (software, information security tools, etc.). However, this leaves a number of particular questions due to the characteristics of a specific automated system. The occurrence of errors in the automated system for the preparation of aircraft flight data can lead to irreparable losses, the most damage is caused by design errors and incorrect general solutions implemented at the stage of system development. This necessitated the identification of specific principles of system design and development. The developed principles of designing an automated system consist, firstly, in determining its reference result, secondly, in identifying the main types of data and ensuring controlling their syntactic and semantic correctness, and, thirdly, in correct defining the boundaries of the system. The theoretical basis for the principles of the development of an automated system is the provisions of the systems approach, in particular, the new application of the system stratification tool. A typical automated data preparation system is considered as an example. It is shown that the use of the proposed principles allows avoiding or minimizing design errors and miscalculations and bringing the system representation stratification to a level that allows obtaining the necessary initial data and evaluating the quality indicators of the output data