NTSA said it would no longer retain already printed logbooks beyond the six-month grace period.
The uproar has forced the authority to issue a formal clarification, even as a KCB banking agent named in the controversy has demanded a public apology from the lawyer.
Motorists will then be required to present the reference number at a KCB branch, where a teller will verify the information in the bank system before guiding them through the payment process.
NTSA has come under scrutiny for proceeding with the implementation of controversial transport regulations.
NTSA details how its mandatory vehicle inspection regime would have operated, a day after suspending its enforcement on private cars.
The authority on Sunday said it had notified police not to demand proof of the mandatory inspection certificate from private vehicles during road checks until further notice.