The company also said it had agreed to withdraw its legal challenge over the huge fine in a case that was adjourned in Lagos High Court to enable the two parties to try to negotiate a settlement.
"Pursuant to the ongoing engagement with the Nigerian Authorities, MTN Nigeria has today made a... Good faith payment of 50 billion naira (USD 250 million)," Johannesburg-based MTN said in a statement.
"In an effort to achieve an amicable settlement, MTN has agreed to withdraw the matter from the Federal High Court in Lagos."
Nigeria, Africa's most populous country, is the MTN group's largest market, where it had more than 62.8 million subscribers by the second quarter of 2015.
MTN was slapped with the penalty in October 2015 after it missed a deadline to disconnect 5.1 million unregistered SIM cards.
The Nigerian Communications Commission (NCC), the country's telecoms regulator, at the time cited security concerns over the inability to trace users in a country plagued by frequent kidnappings and an extremist Islamist insurgency, Boko Haram.
The company issued a profit warning last week and said the Nigerian dispute was a factor in falling earnings.
The fine also led to the resignation of chief executive Sifiso Dabengwa and some Nigerian executives.
Nigeria's four major phone companies have routinely been fined in the past for regulatory infractions but none has received as big a punishment as MTN.
The initial fine of USD 5.2 billion was more than MTN's total sales in Nigeria in 2014 and the equivalent of about 37 per cent of the group's total revenue, according to Bloomberg News.
The NCC and Nigerian government were not immediately available to comment.
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