Virgin Atlantic will also now operate daily flights to Lagos.
However, the AWA will operate only in Abuja airport while the AWA X 2 will operate only in Lagos airport.
The NCAA published a circular that contained the updated schedule for international flight operations on Friday.
According to the circular, which was signed by Musa Nuhu, NCAA director-general, RwandAir has received approval to commence commercial flight operations in the country.
RwandAir will operate on Mondays, Wednesdays, Fridays and Sundays both in the Lagos and Abuja airports and on Saturdays only in the Lagos airport.
Meanwhile, Air Senegal and Emirates, which were previously included in the September 4 list of international airlines cleared for operations by the NCAA, have now been excluded from the updated list
According to the regulatory body, the updated schedule for international flight operations took effect on Friday.