This study extends the important debate on internal control practices (ICP) to third sector of the economy, non-profit organizations (NPOs). The central argument of this study is to investigate factors that influence current practices related to segregation of accounting duties that covers authorization, recording, and custodial functions among NPOs in Malaysia. Four factors were tested based on two categories, organizational characteristics (size and organization age), and governance characteristics (board size and level of auditors� involvement). The study employs questionnaire survey as a method of data collection. In testing the hypotheses, inferential statistic multiple regression analysis was used. Findings suggested that board size and organization age have significant relationships with segregation of accounting duties implemented by the organization. Board size shows the greatest influence in establishing good internal control practices in terms of segregation of accounting duties for NPOs, followed by organization age. It can be concluded that proper guidelines on internal controls should be developed by regulating bodies such as Registrar of Society (ROS). As the majority of NPOs is managed by people with novice accounting knowledge, proper guidelines would help NPOs to strengthen their ICP in managing public funds.

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