This study aimed to determine the spatial distribution patterns of Aphelenchoides besseyi among Oryza sativa seeds on panicle, plant hill, and paddy field spatial scales and to present a three-stage sampling method for estimating the mean density per seed in paddy fields. Living and dead nematodes were extracted individually from 20 seeds sampled from each of five panicles, which were sampled from each of six rice plant hills in each of eight paddy fields, where all plants had leaves exhibiting the 'white tip' symptom. Nested ANOVA indicated that A. besseyi density per seed was significantly different among the eight paddy fields, among rice plant hills in paddy fields, and among panicles in rice plant hills. The proportion of nematode-infested seeds (prevalence) increased and reached an upper limit as the mean density per seed on the panicle scale increased, whereas linear relationships were observed between nematode prevalence and the mean density on plant hill and paddy field scales. Relationships between mean density and mean crowding of nematodes per seed indicated that the nematodes exhibited clumped distribution on each of panicle, plant hill and field scales. Using these relationships, a three-stage sampling plan for estimating nematode density per seed at a specified precision level is presented.