Quantitative information and knowledge on factors controlling organic amendments (OA) application rate has become vital to construct an inventory, to understand the change in soil carbon storage and to make a policy. Using a longitudinal dataset (the Basic Soil Environment Monitoring Project, Stationary Monitoring, 1979-1998, launched by Ministry of Agriculture Forestry and Fisheries of Japan), we (1) described the long-term change in OA application rate in paddy field (PF) and (2) described the joint influence of several factors on average application rate by categorizing the data points into several distinct groups. During the survey period, application rates of total OA and livestock waste compost (LWC) decreased, whereas rice straw residue (RSR) application rate increased. Application rate of LWC varied when data points were categorized in terms of PF use, livestock possession, soil types and part /full-time farmers. The smallest LWC application rate (0.3±0.2 Mg ha^-1 for period between 1994 and 1998) was found among rice-single cropping, poorly drained paddy soils (Gley soils, Muck soils and Peat soils), with no livestock possession part-time farmers. Even among rice-single cropping, the application rate was clearly larger (10.6±0.5 Mg ha^-1for period between 1979 and 1983) for non-poorly drained paddy soils (non-poorly DPS), with livestock possession full-time farmers. Much greater than this was the LWC application rate for other PF use (multiple cropping together with rice or converted paddy field), non-poorly DPS, with livestock possession full-time farmers. Therefore, this study emphasizes the importance of categorizing data points at least in terms of soil type, PF use, livestock possession and part/full-time status, when constructing an inventory, exploring changes in OA application rate and when making a policy.