When designing automated systems for aircraft flight data preparation, many practical problems are solved by introducing either insufficient protection means or their redundancy. Both situations create information security vulnerability. On the basis of a number of publications analysis it is concluded that the basics of information security theory are reduced to the formulation of the main axioms, with the implication that there is currently no complete theory of information security of computer systems. As a result there are many issues, including issues of general nature, requiring some elaboration. The article considers a set of issues related to ensuring information security of the automated system for aircraft flight data preparation. The nature of two basic principles of information protection organization in this system is unraveled. The first principle requires consideration of all aspects related to the problem of ensuring information security of the system, and the second ― optimal control of means of information protection of the automated system of aircraft flight data preparation.