Diagnostic absorption features in hyperspectral data can be used to identify a specific mineral or mineral associations. However, it is unknown how accurate hyperspectral mapping can be for identifying alteration mineral compositions at the resolution required to describe structures such as fossil intrusions, or whether it can accurately quantify the alteration present. This study compared petrographic observation with visible, near-infrared (VNIR), and shortwave infrared (SWIR) hyperspectral remote sensing at laboratory- (centimetre-scale) and aerial- (metre-scale) scales to characterise the abundance of surface hydrothermal rock alteration in and around a shallow fossil intrusion on Pinnacle Ridge, Mt. Ruapehu, New Zealand. We classified a high-resolution aerial hyperspectral image to develop a new surface alteration map using Spectral Angle Mapper (SAM) algorithm. The petrographic thin-section and the laboratory and aerial hyperspectral imaging revealed a spectrum of hydrous alteration phases as indicated by the presence of an absorption feature at 2207 nm. Moderate correlation exists between the depth of the absorption feature at 2207 nm and the point counting-derived alteration percent values, indicating reliability of laboratory-based hyperspectral analytical methods. In contrast, aerial hyperspectral data failed to provide any clear correlations to field-mapped alteration using a band-depth approach, and we interpret this due to ‘oversampling’ of surface (supergene) alteration, spectral mixing, and sensor limitations (e.g., bandwidth, signal-to-noise ratio). The hyperspectral image-derived alteration map, created using supervised image classification, can loosely be translated to a geotechnical map where porosity and permeability play a major role in localizing hydrothermal fluid flow and the formation of alteration mineral associations.