Nigerian President Muhammadu Buhari suspended Ayodele Oke, director-general of the National Intelligence Agency, over the April 12 raid, Buhari aide Femi Adesina said.
When Nigeria's anti-corruption agency raided an upscale apartment in Lagos, Nigeria's largest city, agents found more than $43 million as well as 23.2 million naira (Nigerian currency worth about $76,000) and £27,800 (about $35,000).
At the time, the Economic and Financial Crimes Commission said the funds were suspected to be linked to unlawful activity.
But according to local media reports, Oke eventually admitted his agency was responsible for the cash, saying it was being stored for covert operations.
An investigation has been launched into how the National Intelligence Agency got the money, including who authorized the funds' release to the agency, Adesina said. A panel headed by Nigerian Vice President Yemi Osinbajo will carry out the probe and report to Buhari within the next two weeks, Adesina said.
Nigeria has struggled with corruption and looted funds for decades. The anti-corruption unit has scored a number of cash seizures this year after Nigeria's finance minister announced a new whistleblowing policy in December.