The increasing complexity of transaction processes in every organization, both private and public, has led auditors to develop computer-assisted audit techniques (CAATs). However, potential risks, difficulties, and challenges can hinder the effective implementation of CAATs. The purpose of this study was to examine the factors that influence the effectiveness of the implementation of CAATs in the auditor public sector. The study collected the data by distributing questionnaires to respondents. The sample comprised 225 government auditors in Indonesia, namely the Audit Board of the Republic of Indonesia (BPK). The data were analyzed using the least squares structural equation modeling and importance performance matrix analysis (IPMA). The results show that auditor competence and system quality support the effectiveness of using CAATs. In addition, policies and audit evidence do not affect the effectiveness of CAATs’ use. Other test results using IPMA show that the most critical variable influencing performance is competence in support of increasing the effectiveness of CAATs. These findings indicate that the effectiveness of CAATs use in BPK as a government audit agency requires the support of auditor competence and system quality.