A previous study interpreted extremely ¹³C-depleted excursions of planktonic and benthic foraminifera in last glacial sediments (17,500 to 25,400 cal years B.P.) of the core retrieved from off Shimokita Peninsula and off Hokkaido, Japan, as evidence for periodic releases of methane, arising from the dissociation of methane hydrate. To better understand the formation process of the ¹³C-depleted excursions, we conducted high-resolution natural radiocarbon measurements and biogeochemical analyses. We found highly depleted ¹³C excursions ranging from −10.2‰ to −1.6‰ and −6.8‰ to −1.6‰ in planktonic and benthic foraminifera, respectively. Most of the foraminiferal tests in these horizons were brown, most likely as a result of postdepositional alteration, reflecting the formation of authigenic carbonate on the surface of tests. These alterations were also supported by high levels of Mg-calcite and the acid-leaching test for anomalous foraminifera. To evaluate the carbon sources in the altered foraminifera tests, we quantified the relative contributions of ¹⁴C-free methane-derived carbon sources to the formation of authigenic carbonates in foraminifera with depleted ¹³C excursions using a coupled mass balance isotopic model (¹⁴C/C and ¹³C/¹²C). The radiocarbon ages of both planktonic and benthic ¹³C-depleted foraminifera were approximately 600 to 2000 years older than those of normal tests from nearby horizons. The relative contributions of authigenic carbonates derived from the methane oxidizing process reached to ∼22 wt% for planktonic foraminifera and ∼15 wt% for benthic foraminifera. The δ ¹³C values of methane calculated from the mass balance model were between −29‰ and −68‰ for planktonic foraminifera and between −40‰ and −108‰ for benthic foraminifera, consistent with δ ¹³C values reported for thermogenic and abiogenic methane in global methane hydrate reservoirs. These data consistently suggest that methane-related drastic environmental change occurred in the horizons that included δ ¹³C anomalies. This study provides important information for interpreting geological records of the methane hydrate instability associated with climate.