LLM agents commonly use knowledge-based tools and access their underlying files, databases, and search indexes through tool invocation. This integration improves agents' ability to provide domain-specific services but also introduces the risk of tool-mediated knowledge extraction: source content exposed to an agent for legitimate responses may be progressively recovered from its outputs, enabling reconstruction of the knowledge source behind a target tool. This paper systematically investigates this risk and identifies two challenges introduced by tool invocation: tool-selection uncertainty, where an agent may invoke a competing tool instead of the target tool, and tool-argument compression, where fine-grained query information may be lost when the agent generates tool arguments. To tackle these challenges, we propose ToolSiphon, a query-only extraction attack that introduces two complementary signals: a target-discriminative signal, implemented through Tool Contrastive Analysis, to steer queries toward the target tool; and a response-grounded factual signal, implemented through Evidence Chained Feedback, to mitigate argument compression and progressively expand extraction coverage. Across three types of knowledge-based tools and six domain-specific datasets, ToolSiphon recovers 74.3% of source records on average when coarse-grained information about non-target tools is available, with 83.2% textual recovery and 90.2% semantic similarity. Even without such information, it recovers 66.3% of source records. ToolSiphon also remains effective against representative defenses and on three real-world agent platforms.

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