Nigeria's foreign spy chief Ayo Oke has been suspended after anti-corruption officers found more than $43m (£34m) in a flat in the main city, Lagos, the president's office has said.
Muhammadu Buhari has ordered an investigation into how the spy agency headed by Mr Oke came into possession of the money, his office added.
Mr Oke has not yet commented.
However, unnamed intelligence officials told local media that the money was kept in the flat for covert operations.
Anti-corruption officials have uncovered bundles of cash in Nigeria this year.
Mr Buhari took office in 2015 with a pledge to root out corruption in government.
In a statement, his office said he had also suspended his close aide, David Babachir Lawal, pending an investigation into contracts awarded to deal with the humanitarian crisis in the north-east. The region has been hit by an insurgency by militant Islamist group Boko Haram.
A three-member panel, led by Vice-President Yemi Osinbajo, will investigate both cases, Mr Buhari's office added.
Apart from US notes worth $43.4m, the Economic and Financial Crimes Commission (EFCC) found nearly £27,800 and some 23m naira ($75,000) at the empty flat in Lagos's affluent Ikoyi suburb.
The National Intelligence Agency (NIA), which led by Mr Oke, had laid claim to the money, Mr Buhari's office said.
The panel has been ordered to report within 14 days on who authorised the release of the money to the NIA and whether any laws or security procedures had been breached, Mr Buhari's office added.
Mr Oke would remain suspended pending the outcome of the investigation, it said.
Last week, the EFCC said it carried out the raid after a tip-off that a woman, looking "haggard" and wearing "dirty clothes", was taking bags in and out of the seventh-floor flat.
The "neatly arranged" cash was stashed in "sealed wrappers" in wardrobes and cabinets in the four-bedroom flat, the EFCC added.
In March, it said it had found "crispy" banknotes worth $155,000 at the airport in northern Kaduna city.