NFF President Aminu Maigari says he has not spoken to Stephen Keshi since the coach announced his shock resignation on Monday evening.
Keshi dropped his bombshell during a radio show on Monday in Johannesburg, and Maigari implied that the coach did not show respect.
"I was as surprised as anybody else to hear that he had resigned because I never saw a letter from him. I employed him and there are processes in place for doing things.
If he wanted to resign, he should have shown me respect by informing me the proper way," Maigari tells KickOffNigeria.com.
Despite Keshi having met with Sports Minister Bolaji Abdullahi into the early hours before agreeing to rescind his decision, Maigari said he had not spoken to the coach.
"I haven't talked to him. If he has something to tell me, he should come and tell me."
Abdullahi, however, said he spoke to Maigari before going into his meeting with Keshi. All three are on the same chartered flight taking the team to Abuja, but Keshi and most NFF officials avoided each other all the way to boarding.
Abdullahi admits that some friction remains, but says there will be time to resolve all that.
"This is not the time for that. For now we have resolved the issue and he will be staying. After the reception we will sit down and sort things out. Obviously, there are certain things that weren't handled properly, but we will have plenty of time to sort them out.