Australia has transitioned to primary Human Papillomavirus (HPV) screening; however, high‐risk HPV (hrHPV)‐negative high‐grade squamous intraepithelial lesions and adenocarcinoma in situ have been reported. HPV in situ hybridisation (ISH) testing has been proposed to reclassify these cases. This study identified hrHPV‐negative lesions and assessed HPV‐ISH. A total of 89 of 1468 patients (6.06%) had hrHPV‐negative lesions, and HPV‐ISH revealed five (5.75%) reclassified positive cases. No demographical differences were found between groups. Current population‐level screening is effective. HPV‐ISH was not effective for reclassification. This small, significant population requires further study to assess the phenomenon and augment detection given the implications of misidentification.