The company, with operations in nearly two dozen countries, said it added 7.5% more customers in the first three months of 2014, compared with growth of 14.5% a year ago. It now has 210 million users.
"Our operating environment remains tough, with persistent price competition and regulatory challenges in key markets," chief executive Sifiso Dabengwa said in a statement.
MTN said it disconnected more than 973 000 South African customers that had been showing activity but generating no revenue, reducing the overall number of subscribers to just under 30 million in one of its most lucrative markets.
A month-long ban on SIM card sales in Nigeria for flouting quality standards and slower subscriber growth in Iran also had an impact, MTN said.
MTN added subscribers in most of its other markets, although average revenue per user was on a downward trend, including a 16.5% drop to $9.32 in South Africa.
Its shares had fallen 4.3% by 09:42 GMT at R207.02.