Federal state information systems (FSIS) in Russian agriculture are a key result and driver of digital transformation within the industry. Considering practical application and user needs, FSIS can be improved based on the identified shortcomings experienced by agricultural producers. An online survey was conducted in the first half of 2024, gathering responses from 957 operating agricultural enterprises across all constituent entities of the Russian Federation. The survey focused on experiences using the systems and the problems encountered. The findings confirmed significant issues, with respondents citing concerns about convenience, functionality, and operational stability of FSIS operation. The Unified Federal Information System on Agricultural Lands (UFIS AL), FSIS “VetIS,” and FSIS “Saturn” were identified as particularly problematic, while the National Digital Track System (NDTS) “Chestniy znak” and FSIS “Argus-Fito” were viewed more favorably. To address these challenges, several recommendations are proposed. First, incentivizing investments in digital infrastructure is crucial to accelerate digital transformation. Second, a systematic approach is needed, combining the functions of the systems in a “single window” within a digital ecosystem, and including diverse stakeholders such as the academic community as auditors in the development, implementation, and use of the systems to improve stability. Third, data collection from agricultural producers needs to be modernized to reduce manual input and address the perception of the systems as overly complex. Fourth, more thorough scenario modeling of FSIS use by agricultural producers and government agencies, considering available labor resources, will enhance usability and functionality. The survey indicated that introducing mobile versions (applications) with both online and offline capabilities would be beneficial. Finally, the resulting digital ecosystem should provide sufficient flexibility to address the constraints imposed by existing economic sanctions.