Clinical coordination between primary (PC) and secondary care (SC) is a challenge for health systems, and clinical coordination mechanisms (CCM) play an important role in the interface between care levels. It is therefore essential to understand the elements that may hinder their use. This study aims to analyze the level of use of CCM, the difficulties and factors associated with their use, and suggestions for improving clinical coordination. A cross-sectional online survey-based study using the questionnaire COORDENA-CAT was conducted with 3308 PC and SC doctors in the Catalan national health system. Descriptive bivariate analysis and logistic regression models were used. Shared Electronic Medical Records were the most frequently used CCM, especially by PC doctors, and the one that presented most difficulties in use, mostly related to technical problems. Some factors positively associated with frequent use of various CCM were: working full-time in integrated areas, or with local hospitals. Interactional and organizational factors contributed to a greater extent among SC doctors. Suggestions for improving clinical coordination were similar between care levels and related mainly to the improvement of CCM. In an era where management tools are shifting towards technology-based CCM, this study can help to design strategies to improve their effectiveness.