Steering Over-refusals Towards Safety in Retrieval Augmented Generation

Safety alignment in large language models (LLMs) induces over-refusals -- where LLMs decline benign requests due to aggressive safety filters. We analyze this phenomenon in retrieval-augmented generation (RAG), where both the query intent and retrieved context properties influence refusal behavior. We construct RagRefuse, a domain-stratified benchmark spanning medical, chemical, and open domains, pairing benign and harmful queries with controlled context contamination patterns and sizes. Our analysis shows that context arrangement / contamination, domain of query and context, and harmful-text density trigger refusals even on benign queries, with effects depending on model-specific alignment choices. To mitigate over-refusals, we introduce \textsc{SafeRAG-Steering}, a model-centric embedding intervention that steers the embedding regions towards the confirmed safe, non-refusing output regions at inference time. This reduces over-refusals in contaminated RAG pipelines while preserving legitimate refusals.