Obsidian provenance studies, based on geochemical signatures, are important for determining the source regions of obsidian artefacts. Such research depends on the availability of reproducible geochemical data. An inter-laboratory study was conducted to validate analytical methods applied to samples from four obsidian sources in northeast Hokkaido Island (Shirataki, Rubeshibe, and Oketo regions). The methods applied were Wavelength-Dispersive X-ray Fluorescence (WDXRF), Energy-Dispersive X-ray Fluorescence (EDXRF), Inductively Coupled Plasma–Mass Spectrometry (ICP–MS), Neutron Activation Analysis (NAA) and Prompt-Gamma Activation Analysis (PGAA). Eight laboratories in Japan, the Russian Federation, Republic Korea, Hungary, Canada, and the USA took part in the trials. Results indicate discrepancies between laboratories, but compositional data for 53 elements were successfully compiled, and reference compositions for 16 elements in each sample defined. Based on these data, a new chemical discrimination scheme is proposed for obsidian sources in the Shirataki, Rubeshibe, and Oketo regions. This scheme is applicable to the discrimination of obsidian sources using semi-quantitative EDXRF analysis, with this being important in non-destructive provenance studies of artefacts. This study fosters the further establishment of reference materials for obsidian sources in the Hokkaido region, and the sharing of such materials.