Customers had until the end of October to register their fingerprints and photographs at their local bank.
The bank says messages claiming to help reactivate registration are fraudulent and actually trying to get people's personal information.
Huge sums are allegedly stolen from Nigerian banks as a result of forgery and illegal withdrawals.
Customers who registered were given a Bank Verification Number (BVN) to use at cash machines, and for online and mobile transactions.
Banks are using the verification number along with customers' biometric information to check they are genuine.
Potentially millions of people could now be blocked from these services as less than half of Nigeria's 52 million bank account holders had registered on Friday, according to Central Bank of Nigeria (CBN) spokesman Ibrahim Mu'azu.
On Monday, he released a statement saying that "unscrupulous individuals" are trying to get people to reveal their personal details to use to defraud them.
He wrote that an example message says: "Dear customer, due to the new BVN policy by the CBN your account has been deactivated and to reactivate, callâ€¦â€¦".
He reminded customers that "neither the Central Bank of Nigeria and deposit money banks nor their employees or agents would ever call bank customers or send e-mail/text messages requesting for passwords, card details or personal identification number (PIN)".
Nigeria's central bank has warned that fraudsters are taking advantage of a major crackdown on fake bank accounts.