Along continental margins, various types of methane seeps with a variety of flux rates, spatial extents, and durations occur. Although numerous studies have investigated spatially extensive high-flux-rate seeps, seeps with ephemeral and/or weak flows, known as diffusive seeps, have received less attention. This study investigates ancient diffusive methane seeps in the Shin'etsu sedimentary basin, central Japan, aiming to deduce their spatial extent and their sedimentological, paleontological, and geochemical properties. The seeps were identified as centimeter-scale carbonate concretions in two outcrops of Neogene siltstones in the basin. A comprehensive examination of the spatial distribution of the carbonates, their associated molluscan fossils, petrography, carbon and oxygen isotopic compositions, and lipid-biomarker contents of the concretions revealed that they originated from the anaerobic oxidation of methane (AOM) and formed via a weak, diffusive fluid flow. The small size and irregular or burrow-shaped morphologies of the concretions indicate that methane-bearing fluids diffused through small pore spaces such as burrows. Associated molluscan fossils consist of vesicomyids and other bivalves typical of methane seeps. Fossils of predator species were also identified, but epifaunal seep organisms are notably absent. The carbonate concretions are composed of strongly 13C-depleted micrite (δ13C values as low as −46.0‰ vs. VPDB) with minor 13C-rich void-filling sparry cements. The presence of lipid biomarkers pentamethylicosane (PMI; with δ13C values as low as −119‰) and biphytane and the absence of crocetane suggests that the AOM was performed by an ANME-1-dominated archaeal community. The insights of diffusive methane seepage in the geological record gained from this study can help to better understand depositional processes of seep deposits and variations in fluid flows in both ancient and modern methane-seeping systems.