Special audit powers enable independent audit and may lead to reassessment and recovery based on the auditor's report.

Special audit may be directed, with the Commissioner's prior approval, where an Assistant Commissioner opines declared value is incorrect or input credit is abnormal, requiring the registered person to have records audited by a chartered or cost accountant nominated by the Commissioner. The nominated accountant must submit a signed, certified audit report within the prescribed period, subject to possible extension. The provision applies despite other audits. The registered person is entitled to an opportunity to be heard before material from the special audit is used, and the Commissioner determines and pays the audit expenses. Detection of unpaid or short paid tax or wrongly availed credit may trigger recovery proceedings.

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