The Nigerian Communications Commission (NCC) initially said the $5.2bn fine had been reduced to $3.4bn.
But NCC spokesman Tony Ojobo says the correct amount is $3.9bn (£2.5bn).
The original sanction was imposed in October for failing to cut off unregistered users.
The company has not yet commented.
Since the original fine, the South African company has made a number of senior managerial changes, which included the resignation of the MTN chief executive, Sifiso Dabengwa.
The fine was reduced after MTN complained to the NCC.
"There was a typo. The reduction should have been 25%," Mr Ojobo told the Bloomberg news agency.
"We saw the mistake and had to fix it."
The amount has to be paid by December 31.
MTN has 231 million subscribers in 22 countries across Africa, Asia and the Middle East. However, Nigeria is its biggest market.
In September, the company was named as most admired brand in Africa in the Brand Africa 100 awards, beating Samsung, while it was also awarded the continent's most valuable brand, worth $4.6bn (£3bn).
MTN was South Africa's second mobile operator when it was set up in 1994 after the end of apartheid.
It began its expansion across Africa four years later with operations in Rwanda, Uganda and Swaziland.
Nigeria's telecom regulator says it made a $500m (£330m) typing error when announcing a reduction in a massive fine imposed on Africa's largest mobile operator, MTN.