The Economic and Financial Crimes Commission (EFCC) also held 16 private bank workers for the "mega scam".
The suspects stole "tonnes of defaced naira notes", which were meant to be destroyed, it said on its website.
Newly-installed Nigerian President Muhammudu Buhari has pledged to make tackling corruption a priority.
The arrests were made last week, before the president's official swearing-in ceremony, and so should not be seen as part of Mr Buhari's promised clampdown on corruption, reports the BBC's Will Ross from Lagos.
The move is more likely to be a show of strength from the EFCC, in an attempt to prove its relevance, our correspondent adds.
The Central Bank says it uncovered the problem during an internal audit and handed over the staff to the EFCC.
The suspects allegedly filled boxes supposed to contain damaged currency with bits of newspaper cut into the shape of naira notes, before sending them to branches of the Central Bank of Nigeria for destruction, according to the EFCC.
The actual banknotes were held back so that they could be reused, it adds.
The EFCC suspects the scam of incinerating newspaper instead of old notes has been going on for years and has been on such a scale it has put inflationary pressure on the economy.
Many analysts say the EFCC has been extremely weak when it comes to fighting corruption as low-ranking officials tend to be investigated rather than so-called big fish who appear untouchable, our correspondent says.
The suspects are to make their first appearances at the federal court in the city of Ibadan on Tuesday.
Nigeria's anti-corruption agency has arrested six senior central bank officials over an alleged $33m (£21m) currency fraud.