Nigeria's infrastructure collapsed under the Abacha regime
Anthony Ani said he discovered the missing money while reconciling state accounts for the handover to the new military ruler, General Abdulsalami Abubakar.
Mr Ani said withdrawals were made on General Abacha's personal authority by his security adviser, Ismaila Gwarzo, ostensibly for security purposes.
Mr Gwarzo was recently freed after a three-month detention period.
Some funds were traced to Beirut. Mr Ani said that he had managed to recover $700m.
Collapsed infrastructure
General Abacha's government is thought to have stolen more than $2bn in total.
Nigeria's infrastructure collapsed under the previous military government. Its oil refineries barely operate, the education and health systems have all but fallen apart and the electricity supply is sporadic.
Money that was allocated for the repair of refineries and other infrastructure disappeared or was never released by the government.
The new military government has made some effort to trace funds that went missing under General Abacha's regime.
But the BBC correspondent in Lagos, Hilary Andersson, says it appears to be treading softly, perhaps because many members of the current government, including the head of state General Abubakar, were also senior members of the last government.
Nigeria - one of the world's biggest oil producing nations - generates millions of dollars every day in oil revenues.