The presidency said Ibrahim Lamorde was "proceeding on terminal leave ahead of the formal expiration of his tenure" as chairman of the Economic and Financial Crimes Commission (EFCC) in February next year.
"President Muhammadu Buhari has approved the appointment of Mr Ibrahim Mustafa Magu as the Acting Chairman," the head of state's spokesman Femi Adesina said in an emailed statement.
In August, Lamorde himself was forced to deny claims that $5 billion (4.65 billion euros) went missing at the EFCC and described the allegations as a smear campaign by a politician the agency was investigating.
Earlier today, the former Niger Delta minister under Buhari's predecessor Goodluck Jonathan pleaded not guilty to charges of bribery and false declaration of assets.
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Godsday Orubebe appeared before the Code of Conduct Tribunal accused of failing to declare two properties he owned at the time he took office in June 2011.
He was also alleged to have received bribes amounting to 70 million naira ($350,000, 328,000 euros), the hearing in Abuja heard.
The case was adjourned until November 26.
Orubebe, 56, caused a stir during collation of ballots after the March 28 vote, which saw Buhari and his All Progressives Congress (APC) defeat Jonathan and his ruling Peoples Democratic Party (PDP).
He shouted and attempted a sit-in in a 15-minute stand-off captured live on television at the venue where results were being announced. Orubebe later apologised for his outburst.
The third most-senior political figure in the country, Senate leader Bukola Saraki, is also facing failure to declare assets charges at the same tribunal.
The Niger Delta is home to Nigeria's oil industry. The minister is in charge of development projects in the region, where most people live in poverty despite the multi-billion dollar industry.
Dasuki, who is facing firearms and money laundering charges, was last week allowed to retrieve his passport to go oversees for medical treatment.
But he failed to leave after members of the Department of State Services (DSS) turned up at his house and allegedly prevented him from travelling. He claims his life is under threat.
The DSS denied the claim and said its agents' presence was linked to Dasuki's non-appearance before a committee probing a multi-billion-dollar arms deal during his time in office.