Many-Tier Instruction Hierarchy in LLM Agents

Large language models increasingly operate under multiple instructions from heterogeneous sources with different authority levels, including system policies, user requests, tool outputs, and retrieved context. While prior work on instruction hierarchy highlights the importance of respecting instruction priorities, it mainly focuses on adversarial attacks and overlooks the benign but common instruction conflicts that arise in real-world applications. In such settings, models must not only avoid security violations but also preserve task utility and behavioral consistency when instructions partially or implicitly conflict. We propose Neuro-Symbolic Hierarchical Alignment (NSHA) for hierarchical instruction-following by explicitly modeling and enforcing instruction priorities. At inference time, we introduce solver-guided reasoning that formulates instruction resolution as a constraint satisfaction problem, enabling the model to derive a maximally consistent set of applicable instructions under hierarchical constraints. At training time, NSHA distills solver-based decisions into model parameters using automatically constructed supervision. We evaluate our approach on rule following, task execution, tool use, and safety, covering both single-turn and multi-turn interactions, and show that NSHA significantly improves performance under such conflicts while maintaining competitive utility in reference settings.

LLM agents take instructions from the operator, repository configuration, user, tool results and saved memory, which often conflict. Instruction-hierarchy benchmarks ask whether the higher-ranked source wins, but a source sets position, role and label at once. First, we build WhoWins, 1,080 code-scored scenarios in five task types, each with up to five mutually exclusive instructions, and seven controlled experiments that vary only how instructions are delivered. Second, we study 14 open-weight models (0.6B to 122B, thinking off and on) over 1,887,356 scored replies, checking main findings on held-out scenarios. Inside one message the first of two conflicting lines wins 72.42 to 94.66%, and across messages it keeps 22.95 to 62.65%. A policy sent first in the system (or developer) message loses most conflicts with later lines in every Qwen model but wins most on gpt-oss when it acts. In tool and file-write tasks it wins less often than the same text sent first as a labelled user message, in every model-mode. Third, we test whether pairs forecast larger conflicts; forecasts improve in every model-mode once they know where the task line is. Finally, by our keyword patterns at most 2.92% of decided pair replies flag or hedge a conflict.

As large language model (LLM) based systems take on high-stakes roles in real-world decision-making, they must reconcile competing instructions from multiple sources within a single prompt context. Enforcing an instruction hierarchy, where higher-level directives override lower-priority requests, is critical to the reliability and control of LLMs. In this work, we reframe instruction hierarchy resolution as a reasoning task. The model must first "think" about the relationship between a given user prompt and higher-priority instructions before generating a response. To enable this capability, we construct VerIH, a training dataset of constraint-following tasks with verifiable answers, comprising aligned and conflicting system-user instructions. We show that lightweight reinforcement learning with VerIH effectively transfers general reasoning capabilities of models to instruction prioritization. Our method leads to consistent improvements across multiple model families on both instruction following and instruction hierarchy benchmarks, achieving ~20% absolute improvement in conflict setups. Our method also leads to improved alignment to safety-critical scenarios beyond the training distribution, exhibiting increased robustness against jailbreak and prompt injection, reducing absolute attack success rates by up to 20%. Our results establish reasoning over instruction hierarchies as a practical mechanism for improving AI reliability, where targeted updates to system prompts produce predictable, controllable, and robust changes in model behavior.