The move comes as Nigeria, Africa’s biggest economy, faces recession for the first time in more than 20 years.
The investigation threatens to raise tensions between Nigeria and the South African firm just three months after MTN agreed to pay a reduced fine of 330 billion naira in a settlement with the government over unregistered sim cards.
MTN is the largest mobile phone operator in Africa and Nigeria accounts for around one third of the company’s revenues.
Its shares were down by 4.20 percent, at 1:46 pm local time on the Johannesburg Stock Exchange on Tuesday.