A case control study was conducted to estimate the prevalence of feather-damaging behavior and evaluate the correlation with risk factors among pet psittacine birds in Japan. Although feather-damaging behavior among pet parrots is frequently observed in Japan, its prevalence and potential risk factors have not been investigated. Therefore, we conducted an online questionnaire survey on parrot owners throughout Japan to examine regional differences in feather-damaging behavior and associated risk factors. In total, 2,331 valid responses were obtained. The prevalence of feather-damaging behavior was 11.7%, in general agreement with prior studies. The highest prevalence was among Cockatoos (Cacatua spp., etc.; 30.6%), followed by Lovebirds (Agapornis spp.; 24.5%) and African grey parrots (Psittacus erithacus; 23.7%). Multivariate logistic regression was carried out to calculate the adjusted odds ratio (ORadj) for potential risk factors and adjust the confounding of the variables. The odds of feather-damaging behavior were significantly higher for Conures (Aratinga spp., Pyrrhura spp., Thectocercus acuticaudatus, Cyanoliseus patagonus) (ORadj = 2.55, P = 0.005), Pacific parrotlets (Forpus coelestis) (ORadj = 3.96, P < 0.001), African grey parrots (ORadj = 6.74, P < 0.001), Lovebirds (ORadj = 6.79, P < 0.001) and Cockatoos (ORadj = 9.46, P < 0.001) than Budgerigars (Melopsittacus undulatus), and for young adults (ORadj = 1.81, P = 0.038) and adults (ORadj = 3.17, P < 0.001) than young birds, and for signs of separation anxiety (ORadj = 1.81, P < 0.001). Species, bird age and signs of separation anxiety were significantly higher risk factors for feather-damaging behavior than any other potential risk factors. Our findings, which include broad species diversity, are a good source of data for predicting risk factors for feather-damaging behavior and could be useful in preventing declines in welfare.