Frugivorous birds are the primary seed dispersers for fleshy-fruited plants through defecation. In general, small-sized species disperse seeds across short distances from parental plants. However, multiple seeds or seeds of different plant species are frequently mixed in the fecal mass, because birds are prone to eat multiple fruits of a few plant species during foraging. This suggests birds deposit seeds as clumps in the field, causing inter- and intraspecific competition. However, the exact number of dispersed seeds for each defecation is very hard to estimate in field. It may also vary according to several variables, such as body size of birds and number of seeds per fruit. To clarify seed deposition patterns, we captured small frugivorous birds and collected the feces and regurgitations. The number of seeds excreted in fecal samples was investigated. From 2003 to 2019, a total number of 21518 seeds from 60 plant species were collected from 2214 birds of 17 species. Average number of seeds included in the fecal sample was 9.7 ± SD 18.4 (range: 1–340). The frequency of the number of excreted seeds was not normally distributed and the mode value was one in all cases and for five main dispersers. In most cases (64.8–74.5%), birds excreted a single seed. Furthermore, the effects of morphological traits of birds and plants on number of excreted seeds were analyzed using GLMM. The body mass of birds had a positive effect on the number of excreted seeds. However, fruit and seed weight exhibited negative effects, suggesting the number of excreted seeds is smaller when smaller birds eat larger fruits bearing larger seeds. The seed deposition pattern based on excretion of a single seed may avoid seed and seedling aggregation at local sites.