MTN said in a statement on Friday there had been allegations that a top official in the Nigerian presidency took a payment towards reducing the fine.
The telecom group was initially fined $5.2 billion last October for failing to deactivate more than five million unregistered SIM cards.
In June, MTN agreed to pay a reduced fine of 330 billion in a settlement with the Nigerian government and said the fine will be paid by MTN Nigeria over three years.