Hallucinations in large language models (LLMs) pose significant safety concerns that impede their broader deployment. Recent research in hallucination detection has demonstrated that LLMs' internal representations contain truthfulness hints, which can be harnessed for detector training. However, the performance of these detectors is heavily dependent on the internal representations of predetermined tokens, fluctuating considerably when working on free-form generations with varying lengths and sparse distributions of hallucinated entities. To address this, we propose HaMI, a novel approach that enables robust detection of hallucinations through adaptive selection and learning of critical tokens that are most indicative of hallucinations. We achieve this robustness by an innovative formulation of the Hallucination detection task as Multiple Instance (HaMI) learning over token-level representations within a sequence, thereby facilitating a joint optimisation of token selection and hallucination detection on generation sequences of diverse forms. Comprehensive experimental results on four hallucination benchmarks show that HaMI significantly outperforms existing state-of-the-art approaches.