MTN was fined for non-compliance with a deadline set by the NCC to disconnect all non-registered sim cards.
The move follows accusations by mobile phone users that the regulator had failed to bring operators to account for poor services to subscribers.
MTN Nigeria says it is studying the letter sent to it by the regulator and will respond soon.
MTN is one of the largest phone providers in Nigeria.
A senior official of the company told the BBC it was in talks with the regulator over the fine and hoped to resolve the matter.
BBC Abuja editor Bashir Sa’ad Abdullahi says some Nigerians say they want the regulator to address poor network signals provided by telecoms companies in the country.
They want more sanctions on firms to encourage them to improve signals and the quality of service in the country, he says.
Statistics from the NCC indicates that Nigeria, a country with an estimated population of more than 170 million, has almost 150 million mobile phones.