The contingent had been booked into the Sheraton Hotel and Towers in Abuja, but rejected the accommodation and decided to move to the Transcorp Hilton instead.
An NFA official attached to the team informed KickOffNigeria.com that the South Africans were allocated rooms with king-sized beds, but their officials requested twin-beds instead.
"While the hotel was making arrangements to accommodate their request, they left and went to Transcorp Hilton without informing us," the official says.
NFA Secretary general Bolaji Ojo-Oba on Saturday told KickOffNigeria.com that an apology had been tendered and accepted.
"We confronted them and asked why they changed hotels without informing us. There is nothing sub-standard about the Sheraton Hotels. Sheraton is Sheraton everywhere and their standards are the same.
"We were already making arrangements to meet their request when they decided to leave and go to another hotel. But we spoke to them and they apologised, and we have accepted their apology.
"We are very good hosts and we always treat visiting teams very well. Nobody can say that the Sheraton Hotel is not good. That is where we used to lodge our former coach Mr Berti Vogts and he never complained."
Nigeria play South Africa on Sunday at the Abuja National Stadium.