The Director General, NOTAP, Dr Dan-Azumi Ibrahim said this in an interview with newsmen in Abuja.
He said that what the agency had approved for the bank was software licence agreement and not management franchise agreement.
The News Agency of Nigeria (NAN) recalled that the issue started few months ago when shareholders of Stanbic IBTC wrote a petition drawing the attention of regulatory authorities to some unapproved transactions entered into by the bank.
They alleged that billions of naira deducted from gross revenue earned, had been illegally stashed in suspense account since 2011.
They alleged that the amount was to pay the bank's controlling shareholder, Standard Bank of South Africa for franchise and management fees without prior approval from NOTAP which is mandatory.
The NOTAP boss explained that his office had no intention of approving a franchise agreement licence for Stanbic IBTC because it was not needed in Nigeria.
"I want to categorically say that we have not approved franchise agreement for Stanbic IBTC bank.
"What was approved for them in 2012 was software licences agreement. It's like any other bank. Most of the banks are enjoying that facility.
"They were given approval for three years, from 2012 to 2015, and by now, I think the certificate might have expired.
"But as far as franchise is concerned, we have not given approval to them. And we categorically made it clear to them that we are not going to give franchise fee agreement approval," he said.