In order to help maintain soil fertility, a national survey was conducted in Japan, beginning in 1979. Both soil samples and questionnaires given to farmers on agricultural management were collected. By using the dataset, we described the long-term application rates of on-farm organic amendments (which we denote as OA and consists of livestock waste compost (LWC), and “other OA” such as rice straw residue) that are crucial for maintaining soil fertility. Average LWC and “other OA” application rates (fresh weight, FW) decreased from 17.8 ± 0.5 and 3.2 ± 0.2 (1979-1983) to 12.1 ± 0.4 and 2.7 ± 0.4 (1994-1998) Mg Fw ha^-1, respectively. The long-term change in LWC application rate may be partly due to limited time and labor. The application rates were influenced by the type of crop, possession of livestock, and the part-time/full-time status of farmers. The differences in OA application may be partly due to the separation of crop and livestock farming. When data points were categorized by the joint influence of these factors, there was a difference of more than seven times between the largest and smallest LWC application rates. The largest application rate was achieved by the group with “feed and forage crops” (FFC, such as dent corn) along with full-time farmers possessing livestock, while the smallest rate was achieved by the group of full-time or part-time farmers with neither FFC nor vegetable cropping (e.g. potatoes), and with no possession of livestock.