The appointments of top civil servant Babachir Lawal and Ayo Oke, director-general of the National Intelligence Agency, were terminated with “immediate effect”, a statement said.
Both men had been suspended since April.
Lawal, who as Secretary to the Government of the Federation was Nigeria’s most senior public official, was accused of a contract scam for rebuilding the conflict-scarred northeast.
He is alleged to have awarded deals for reconstruction in areas hit by Boko Haram’s Islamist insurgency to companies in which he had a personal interest.
Oke was removed after the discovery of some $43 million (37 million euros) in cash at a private residence in an upscale area of the commercial hub of Lagos.
The money was claimed by the NIA.
President Muhammadu Buhari, who was elected in 2015 on a promise to tackle corruption, has come under fire since taking office for targeting political opponents.
But the main opposition Peoples Democratic Party has accused him of a witch-hunt, as the overwhelming majority of those arrested and charged are PDP supporters or former ministers.
The Lawal and Oke cases have been seen as a litmus test of his commitment to prosecuting graft, regardless of political allegiances.
Buhari’s deputy, Vice-President Yemi Osinbajo, submitted a report into the claims in August.
The presidency has recently been embroiled in a scandal involving an indicted civil servant who went on the run after being accused of stealing two billion naira ($5.6 million).
The official managed to avoid arrest and return to Nigeria, where he was reappointed to the civil service. Buhari last week ordered his dismissal and arrest.