The Presidency had earlier described the report of Magu's sack as "speculative" and "preemptive."
The report of Magu's purported sack was first reported by The Guardian on Saturday, December 31.
Presidential spokesmen, Garba Shehu and Femi Adesina have in separate statements on twitter denied the report, describing is as "speculative" and "preemptive."
The EFCC via Twitter maintained that Magu remains the head of the Commission.
"Guardian Newspaper Lied. Magu Not Sacked!," the anti-graft agency wrote.
Magu’s nomination was recently rejected by the Senate following allegation of graft levelled against him by the Department of State Security Service (DSS).