The article deals with the problem of managing medical information systems, including the example of quality control of the provision of medical services using isotope-containing medical materials. A digitalization of economics leads to a strong transformation of business routines of companies in wide variety of industry branches. The transition from paper media to electronic document management systems all over the world is associated with a complex of methodological and organizational and technical tasks to ensure the availability and reliability of data, regulatory support for the interactions of all participants in the process of collecting, transferring, processing and storing information, as well as the formation of an archive of data of former periods. The mathematical model allows at the practical level to carry out multi-parameter monitoring and control in the main critical areas. The use of a qualitative assessment in parallel with a quantitative one allows the managing staff of the administration of a medical institution to obtain a more complete assessment of the situation in controlling the circulation of isotope-containing materials in the provision of medical services to the population. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.