See The Steps Below On How To Pay For Nigerian E-passport:

Nigerian Passport Application Payment Procedures
To make Payment, you need to
go to >>>>>> https://portal.immigration.gov.ng/passport/passportPaymentStatus,
put in your Nigerian Passport Application ID and Reference Number,
Click on SEARCH,
Then Proceed to Payment.
It will ask you to log in ( Log in with the email and password you used in filling your Nigerian Passport Application Form)

Proceed to Payment
Fill in the Payment and Credit Card or Debit Card details.
Make you Payment
Print the ePassport Payment Slip and ePassport Acknowledgement Slip