This paper aimed to clarify factors influencing environmental conflict occurrence during the planning stage for wind farm projects in Japan. After studying conflict occurrence situations and the main conflict issues for 155 large-scale projects across Japan, we focused on both physical and social factors as explanatory variables and applied a quantitative method using binary logistic regression analysis. The main findings were: (1) environmental conflicts had occurred in 59 projects as of May 2012 and the main issues could be classified as noise/infrasound, sediment-related disaster/hydrology, landscape, nature destruction and birds (esp. raptors); (2) turbine number and size were influential factors as structural aspects, while there was no significant association between proximity to turbines and conflict occurrence; (3) sites located within natural parks, national protection forests, sediment-related disaster hazardous areas and wildlife protection areas designated by relevant acts and ordinances showed higher conflict occurrence, and proximity to such areas could be influential as well; (4) habitats for Golden Eagle, Mountain Hawk Eagle, White-tailed Eagle and Steller's Sea Eagle significantly encouraged conflict; (5) in terms of social aspects at both the national and prefectural level, conflict occurrence was strongly associated with the existence of past conflict experiences and complaints about noise and/or infrasound generated by operating wind farms.