This study aims to investigate whether apparatus competence, whistleblowing system, and morality play a role in influencing fraud prevention. It is also intended to prove whether whistleblowing system has a mediating effect on the relationship among apparatus competence, morality and fraud prevention. The research subjects comprise of civil servants of Government Institutions of Central/Provinces/Regencies/Cities in Indonesia. The hypotheses were tested on 201 respondents who were selected using convenience sampling method. The data were collected using survey questionnaires sent via online using Google Form from January to February 2021. The data were analyzed using Structural Equation Modeling - Partial Least Square (SEM-PLS). The results of this study showed that whistleblowing system and morality influenced fraud prevention. Nevertheless, it appeared that apparatus competence did not influence fraud prevention. This study also proves that whistleblowing system has a mediating effect on the relationship among apparatus competence, morality and fraud prevention. Penelitian ini bertujuan untuk mengetahui pengaruh kompetensi aparatur, sistem whistleblowing, dan moralitas terhadap pencegahan fraud dengan peran mediasi sistem whistleblowing. Responden penelitian terdiri 201 Aparatur Sipil Negara (ASN) pada pemerintahan Pusat/Provinsi/Kabupaten/Kota di Indonesia. Pengumpulan data dilakukan dengan menggunakan kuesioner Google Form yang disebarkan secara online. Data dianalisis dengan menggunakan SEM-PLS (Structural Equation Modeling - Partial Least Square). Hasil penelitian menunjukkan bahwa sistem whistleblowing dan moralitas berpengaruh terhadap pencegahan fraud sedangkan kompetensi aparatur tidak memiliki pengaruh terhadap pencegahan fraud. Hasil pengujian juga menyatakan bahwa sistem whistleblowing memiliki efek mediasi terhadap masing-masing hubungan antara kompetensi aparatur dan moralitas dengan pencegahan fraud. Implikasi penelitian ini dapat dijadikan dasar pada kebijakan manajerial terhadap sistem whistleblowing yang perlu dikembangkan dalam organisasi.