Urinary and fecal incontinence as well as skin pressure injury are common healthcare problems in nursing home; however, these prevalence and related risk factors were not well understood in the Japanese special elderly nursing home settings. We surveyed the prevalence of urinary, fecal and double incontinence, and skin pressure injury among the elderly living in special elderly nursing home in Japan. A nationwide cross-sectional epidemiological survey was conducted with a total of 4,881 residents. The prevalence of urinary, fecal and double incontinence was 82.9%, 68.9% and 64.9%, respectively. Skin pressure injury was found in 283 residents (283/4881, 5.8%). Age, Care-Needs level, loss of voiding desire, and fecal incontinence were significant risk factors for urinary incontinence. Residential period, Care-Needs level, loss of voiding and defecation desires, and urinary incontinence were significant risk factors for fecal incontinence. Only male sex was a significant risk factor for skin pressure injury. Our study revealed continence status and the prevalence of pressure skin injury among older adult residents who receive an end-of-life care in special nursing homes in Japan. Further studies should be conducted to examine whether recovery of urinary and fecal sensations improves continence status.