Nigeria's communications regulator slapped a $3.90-billion fine on the firm in October. MTN has since paid $250-million of it.
The affair cast a shadow over the visit by President Jacob Zuma and was expected to be high on the agenda when he met Buhari for talks in Abuja.
In his first comments on the issue, Buhari told a joint news conference: "The concern of the federal government was basically about the security, not the fine imposed on the MTN. You know how the unregistered GSM [simcards] are being used by terrorists. That was why [the] NCC [Nigerian Communications Commission] asked MTN, Glo and the rest of them to register them.
"Unfortunately MTN was very slow and contributed to the casualties. That was why the NCC looked at its regulations and imposed the fine on them."