Undesirable behaviors exhibited by dogs are called canine behavioral problems. Behavioral problems are common among dogs kept in ordinary homes; hence, veterinarians need to have sufficient knowledge of these problems, so as to advise owners. Among dogs kept in ordinary Japanese homes, only a few behaviors have been investigated regarding prevalence and relevant factors. To improve understanding of behavioral problems, a comprehensive survey is crucial. In this study, we distributed an online survey including general information and questions about 25 canine behaviors that can become problematic to owners, to investigate (1) the prevalence of behavioral problem, (2) the most common behavioral problems, and (3) the relevant factors of each behavior. We collected 2,050 valid responses. Among all dogs, 86.0% exhibited at least one behavioral problem. “Barking at noises inside the house”, “Barking at unfamiliar visitors”, and “Pica” were the most frequent behavioral problems. To reveal those factors related to the expression of each behavior, we performed multiple logistic regression analyses, with the presence of behaviors as objective variables and dogs’ general information as explanatory variables. Breed, age, the presence of other dogs in the household, sex, neutering status, source of acquisition, and type of residence were associated with 19, 16, 5, 4, 4, 4, and 1 behaviors, respectively. This study revealed the prevalence of 25 canine behavioral problems in Japan and relevant factors of each behavior. Our findings will be useful for veterinarians in advising owners about preventing behavioral problems.