Invisible Threats from Model Context Protocol: Generating Stealthy Injection Payload via Tree-based Adaptive Search

Computer Science > Cryptography and Security [Submitted on 25 Mar 2026] Invisible Threats from Model Context Protocol: Generating Stealthy Injection Payload via Tree-based Adaptive Search Yulin Shen, Xudong Pan, Geng Hong, Min Yang Recent advances in the Model Context Protocol (MCP) have enabled large language models (LLMs) to invoke external tools with unprecedented ease. This creates a new class of powerful and tool augmented agents. Unfortunately, this capability also introduces an under explored attack surface, specifically the malicious manipulation of tool responses. Existing techniques for indirect prompt injection that target MCP suffer from high deployment costs, weak semantic coherence, or heavy white box requirements. Furthermore, they are often easily detected by recently proposed defenses. In this paper, we propose Tree structured Injection for Payloads (TIP), a novel black-box attack which generates natural payloads to reliably seize control of MCP enabled agents even under defense. Technically, We cast payload generation as a tree structured search problem and guide the search with an attacker LLM operating under our proposed coarse-to-fine optimization framework. To stabilize learning and avoid local optima, we introduce a path-aware feedback mechanism that surfaces only high quality historical trajectories to the attacker model. The framework is further hardened against defensive transformations by explicitly conditioning the search on observable defense signals and dynamically reallocating the exploration budget. Extensive experiments on four mainstream LLMs show that TIP attains over 95% attack success in undefended settings while requiring an order of magnitude fewer queries than prior adaptive attacks. Against four representative defense approaches, TIP preserves more than 50% effectiveness and significantly outperforms the state-of-the-art attacks. By implementing the attack on real world MCP systems, our results expose an invisible but practical threat vector in MCP deployments. We also discuss potential mitigation approaches to address this critical security gap. Subjects: Cryptography and Security (cs.CR); Artificial Intelligence (cs.AI) Cite as: arXiv:2603.24203 [cs.CR]   (or arXiv:2603.24203v1 [cs.CR] for this version)   https://doi.org/10.48550/arXiv.2603.24203 Focus to learn more Submission history From: Yulin Shen [view email] [v1] Wed, 25 Mar 2026 11:24:47 UTC (1,031 KB) Access Paper: HTML (experimental) view license Current browse context: cs.CR < prev   |   next > new | recent | 2026-03 Change to browse by: cs cs.AI References & Citations NASA ADS Google Scholar Semantic Scholar Export BibTeX Citation Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Demos Related Papers About arXivLabs Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)