President Bola Tinubu has ordered a full forensic audit of IPPIS and other federal government systems.
The move follows concerns over ghost workers, fake agencies and possible gaps in government payroll controls.
The directive was issued after the Federal Executive Council reviewed findings from the Independent Corrupt Practices Commission.
Finance Minister Taiwo Oyedele will coordinate the audit alongside relevant government officials.
The review will examine the Integrated Personnel and Payroll Information System and related financial platforms.
Officials will check how ghost workers and other ineligible persons were added to government payrolls.
The audit will also review identity checks, bank details and controls used to approve government payments.
Investigators will examine connections between IPPIS, GIFMIS, Remita, TSA and Sub-TSA systems.
The goal is to determine whether fraud resulted from system weaknesses or deliberate manipulation. A second part of the exercise will focus on federal ministries, agencies, commissions and parastatals.
Officials will verify the legal status of government bodies and confirm which agencies legitimately receive public funds.
The review will also examine procurement, internal audits and other controls within government institutions.
The forensic audit of IPPIS is expected to expose gaps that may have allowed public funds to be misused.
The Presidency said the exercise must be conducted with independence, professionalism and forensic integrity.
The audit team will work with the ICPC on ongoing investigations, prosecutions and possible recovery of public funds.
