Dozens of charges
Local television stations reported the suspects were paraded in court on Monday afternoon.
Some of the bank chiefs face between 11 and 24 charges, television stations said.
All the bank chiefs deny the charges.
One of them, Cecilia Ibru, the former head of Oceanic Bank, who faces 25 charges, slumped in the court's witness box but was immediately given medical attention.
The heads of the five distressed banks were sacked on August 14 by the Central Bank of Nigeria (CBN) for mismanagement and running the institutions into insolvency.
The CBN said the total loan portfolio of the five banks - Afribank, Intercontinental Bank, Union Bank, Oceanic Bank and Finbank - stood at $17.8bn.
The CBN later published a list of prominent Nigerians as debtors of the distressed banks, prompting the EFCC to give them up to last Wednesday to pay up or face arrest and prosecution.
At the expiration of the deadline, the EFCC said it had arrested 16 bank directors and 68 debtors.
It also said it recovered about $166.5m in debts.
The EFCC also said it would enlist the support of Interpol to arrest those on the run.
Judge Dan Abutu on Monday ordered lawyers of the accused bank chiefs to submit written bail applications to the court on Friday, AIT television said.