This study determined the challenges of comprehensive account auditing and the rampant use of accounting software. Specifically, the study determined the effect of accounting software over efficient bookkeeping and documentations as regards to sufficient audit evidence after comprehensive account auditing. The study also ascertained the effect of complacency in filing and bookkeeping common with firms that rely on accounting software in relation to misstatement, accounting error, fraud and corruption among the top managers and accountants. Finally, the study shall throw a spot light on accounting efficiency among firms. Three research questions guided the study. The design adopted for this study was descriptive survey and correlational research design. The study population comprised76 accountants in the 19 ministries in Anambra State. Mean and standard deviation were used to analyze the research questions. The instrument was validated by experts in accounting and Cronbach Alpha was used to determine the reliability of the instrument which obtained an overall reliability coefficient of 0.79. The study concluded that quality audit reveals the true profitability nature of a company in relation to its total assets, business transactions are lacking in source documents often called business paper due to the use of accounting software, absence of sufficient audit evidence from source documents has negative implications during software accounting audit; and auditors lack sufficient audit evidence from source documents during software accounting audit. The study therefore recommended proper book keeping, documentation and utilization of source documents to check mate system entries, constant periodic internal audit, which help to check the duties and activities of the staff. The study also recommended that constraint should be placed on the accessing of the software according to specific job descriptions, constraint should be placed on amendments and modifications of entries except on authorization and must be manned from the IT department and a manual record of all signed and approved amendments and modifications done, must be kept for reference purposes and during audit.
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