One of the main directions of management development in current conditions has become the massive use of the latest computer and telecommunications equipment and the formation of highly efficient information technologies. Information technology, information systems, and high-productivity technologies are the key systems of the innovation economy. These technologies are fundamentally changing all ways of receiving, processing, transmitting, and producing information and are fundamentally technologizing intellectual activity. Hence the exceptional importance of building reliable and functionally secure information systems, the central element of which is software. The paper presents models and metrics of software quality, considers issues of ensuring functional reliability, shows the relationship between functional and information security of critical information systems for facilities with an increased risk of operation, and presents a comprehensive model for determining the probability of parrying any information attack from a stream of attacks. The presented approaches are used to develop top-level systems for automated process control systems for nuclear power plants.