The moves to prop up the sector came after it was revealed that Nigeria's banks had amassed a staggering $7.6bn worth of bad loans. The heads of Afribank, Finbank, Intercontinental Bank, Oceanic Bank and Union Bank were all removed and could even face criminal charges.
Central bank governor Lamido Sanusi said lax governance had left the banks so weakly capitalised that they posed a threat to the entire banking system.
Nigeria's anti-corruption police said last month it was seeking 19 banking executives for questioning. It said three had already been brought in while the others were "watch-listed" to try to stop them leaving the country.
"We have threatened to declare them 'wanted' because we have been looking for them since yesterday. We have been able to find three," economic and financial crimes commission spokesman Femi Babafemi said.
Nigeria's central bank also published a list of the largest defaulting customers of the five banks and warned the debtors to pay up or face legal action.
The list of more than 200 companies, individuals and state bodies includes stockbrokers, local oil and gas groups and well-known Nigerian companies.
Central bank governor Lamido Sanusi has promised to prosecute anybody found guilty of misconduct. "Anybody, managing director, executive director, director, officers, debtor, anybody that is found that has broken the law will be prosecuted to the full extent of the law," he said.