Agile methods have gained wide popularity recently due to their characteristics in software development. Despite the success of agile methods in the software maintenance process, several challenges have been reported. In this study, we investigate the challenges that measure the impact of agile methods in software maintenance in terms of quality factors. A survey was conducted to collect data from agile practitioners to establish their opinions about existing challenges. As a result of the statistical analysis of the data from the survey, it has been observed that there are moderately effective challenges in manageability, scalability, communication, collaboration, and transparency. Further research is required to validate software maintenance challenges in agile methods.