Security and possible risks of e-health system have been assessed by relevant governmental agencies and involved professionals, including World Bank specialists. Personal data in the system is maintained on the equipment from leading manufacturers', the connection to the system is protected and encrypted, which guarantees data protection and security.

Access to the e-health system is accoumplished by using only strict identification mechanisms. The strict identification of the individual is carried out by identification card (ID) given by the RA Police  through an automated process of identifying the identity of the person with the certificate previously issued individually for that person with the use of software and hardware tools of the Public Keys Infrastructure (PKI) by the only accredited certification center of the Republic of Armenia, the "Electronic Management Infrastructure Implementation Unit" CJSC.

The system is protected from unauthorized access and attacks with the best tools available in the field. The e-health system software is developed by the internationally leading technology company, Ericson Nicola Tesla. They are periodically updated, taking into account the latest technological developments.

Software maintenance, uninterrupted operation of the system software, continuous improvement of software tools, acquisition of software updates are implemented by "National Electronic Healthcare Operator" CJSC.