This study focused on the total precipitable water (TPW) products of the Advanced Microwave Scanning Radiometer 2 (AMSR2) onboard the Global Change Observation Mission—Water (GCOM-W). The GCOM-W satellite has been flying in the Afternoon Constellation (A-train) orbit to synergize with other A-train satellites, such as Aqua. In this study, we compared two datasets of AMSR2 TPW from July 2012 to December 2020, independently produced by the Japan Aerospace Exploration Agency (JAXA) and Remote Sensing Systems (RSS). There were no significant differences in TPW anomaly trends between them. However, significant differences in the absolute values of TPW were found in the northwest Pacific and northwest Atlantic Oceans during the boreal summer season. We investigated the meteorological conditions that caused these differences using reanalysis, in-situ observation data, and visible and infrared data from the MODerate resolution Imaging Spectroradiometer (MODIS) on the Aqua. The results showed that the lower atmosphere had an inversion layer with relative humidity close to 100 %, and very low altitude clouds (i.e., fog) were often distributed in the areas where the TPW differences between JAXA and RSS are large. The temperature profiles represented in the JAXA and RSS algorithms were approximated by a simple model. The influence of the inversion layer and fog on the JAXA and RSS TPW algorithms was also investigated using a radiative transfer model. Sensitivity experiments suggested that the inversion layer was associated with the underestimated TPW for the JAXA algorithm, while it was associated with the overestimated TPW for the RSS algorithm.