From 2016 to 2022 we completed a second survey of "The Wintering Bird Atlas of Japan". With the cooperation of 396 participants, 105,660 questionnaires were collected across Japan, and combined with 788,148 data from other sources and databases. The information was aggregated into a national set of grid cells of approximately 40 km square, and compiled as a distribution map. We release this dataset to provide data to researchers and conservationists who wish to conduct various analyses to evaluate the distribution of birds in Japan during this period.