Safety is a paramount concern in clinical chatbot applications, where inaccurate or harmful responses can lead to serious consequences. Existing methods—such as guardrails and tool-calling—often fall short in addressing the nuanced demands of the clinical domain. In this paper, we introduce TACOS(Taxonomy of Comprehensive Safety for Clinical Agents), a fine-grained, 21-class taxonomy that integrates safety filtering and tool selection into a single user intent classification step. TACOS covers a wide spectrum of clinical and non-clinical queries, explicitly modeling varying safety thresholds and external tool dependencies. To validate our taxonomy, we curate a TACOS-annotated dataset and perform extensive experiments. Our results demonstrate the value of a new taxonomy specialized for clinical agent settings, and reveal valuable insights about train data distribution and pretrained knowledge of base models.