Large language models (LLMs) for code are typically trained to align with natural language instructions to closely follow their intentions and requirements. However, in many practical scenarios, it becomes increasingly challenging for these models to navigate the intricate boundary between helpfulness and safety, especially against highly complex yet potentially malicious instructions. In this work, we introduce INDICT: a new framework that empowers LLMs with Internal Dialogues of Critiques for both safety and helpfulness guidance. The internal dialogue is a dual cooperative system between a safety-driven critic and a helpfulness-driven critic. Each critic provides analysis against the given task and corresponding generated response, equipped with external knowledge queried through relevant code snippets and tools like web search and code interpreter.