The effectiveness of hospital institutions has been maximized due to the implementation of computerized management systems. The objective of this research was to identify the perception of managers and users regarding the Brazilian government program to implement a hospital information system (AGHU) for the management of federal university hospitals. The survey strategy was adopted, obtaining a total of responses from 736 employees from 21 hospitals. Frequency distribution and semantic differential reduction measure, and content analysis were used for data analysis. The results refer to a set of intervening aspects that acted as obstacles to the implementation process, at macro, meso and micro levels. These aspects are configured in different ways in each hospital institution, influencing the system implementation process. This fact reinforces the diversity of the political, cultural and structural context of each institution and the lack of homogeneity in relation to the actions to introduce the AGHU in the different university hospitals. The perceptions of managers and users are aligned with most of the intervening aspects and the results of the process. There was a tendency to agree on the contributions of AGHU to improve the quality of the care process, management processes and productivity.