The move has enabled a monthly saving of around $11,5m (£8m).
The audit is part of an anti-corruption campaign by President Muhammadu Buhari, who took power last year.
Corruption and mismanagement have long been a challenge to Nigeria’s growth, and the government has promised to cut costs to face an economic slowdown.
Nigeria is Africa’s biggest economy and the continent’s top oil producer, and its finances are under strain due to the recent collapse in oil prices.
The country has also faced rising inflation, a stock market slump and the slowest pace of economic growth in more than a decade.
The audit started in December used biometric data and a bank verification number to identify holders of bank accounts into which salaries were being paid, Reuters news agency reports.
This process allowed the identification of some workers who were receiving a salary that did not correspond to the names linked to the bank accounts.
- Africa’s largest economy, biggest oil producer and most populous nation
- Oil-rich, but facing worst economic crisis in years after falling oil prices
- 62.6% of its 170 million population live in poverty
- Average annual earnings – $1280 (£850)
It also revealed that some employees were receiving salaries from multiple sources.
Some 23,846 non-existent workers were removed from the payroll, an adviser to the finance minister was quoted by Reuters as saying.
Periodic checks and electronic audit techniques will be periodically carried out to prevent new frauds, the ministry said.
Officials have said the savings resulted from the anti-corruption measures will help the country tackle its crisis and prevent job cuts.