The commission's investigatory mandate is executed by the investigation department, as directed by section 21 of the Anti-Corruption Commission Act 2008. The Maldivian Penal Code 2014 defines corruption as a crime. The investigation department conducts criminal investigations on the offenses of corruption stated in the Penal Code and electoral corruptions outlined by section 74 of the Election Act 2008. If the commission is alerted of any of these offenses occurring at any institutions under its jurisdiction, the investigative department will investigate the matter.

Once a complaint is lodged to the Commission, its formally registered and evaluated. Based on preliminary findings and evaluation report Commission Members decide whether the complaint need to be investigated or not. If there is no offense of corruption, the case is dismissed. If the complaint is considered to investigate, is transferred to the investigation units. The complaint gets assigned to one of the investigation teams and given an investigation number. The case is investigated by gathering pertinent documents and evidence, summoning suspects and prospective witnesses for questioning, and conducting more research in to the case. Following the conclusion of the investigation, an investigation report is written based on the findings and evidences gathered. The investigation report is presented to the Members of the Commission, who then reach a decision on the case. If the case involves corruption, it is forwarded to the Prosecutor General’s Office for prosecution.