Beyond Over-Refusal: Defending Indirect Prompt Injection via Latent Instruction Manifolds

Large Language Models (LLMs) have been integrated into complex ecosystems (e.g., Code Agents), while Indirect Prompt Injection (IPI) attacks have emerged as critical barriers to their safe deployment. Attackers exploit LLMs' indistinguishability between "instructions" and "data" to manipulate LLMs via maliciously injected instructions. Existing defenses, however, face an intractable safety-utility trade-off: most guardrails either incur high latency or suffer from severe over-refusal. In this paper, we first demonstrate that LLMs can separate instruction from data intrinsically with both theoretical and empirical evidence. Inspired by this insight, we propose AEGIS (Adaptive Ensemble Guard for Injection Shielding). AEGIS extracts instruction-sensitive projectors to identify malicious instructions and leverages a Unified Multi-Layer Consensus mechanism that aggregates topologically distinct signals across the network depth. Empirical evaluations show that AEGIS achieves remarkable detection performance against both heuristic and optimization-based attacks compared to baselines, highlighting its potential to mitigate IPI. Code is available at https://github.com/xaddwell/AEGIS