The forward was called up by head coach of the Nigerian national team, Stephen Keshi alongside 31 others but he failed to turn up or give any reason for his decision.
The 31-year-old striker made his senior international debut against Venezuela two months ago and was set to be included in a 23-man Super Eagles squad for the Cup of Nations between January 19 and February 10.
But once Ameobi was chosen in a provisional Nigerian squad, the Newcastle United manager, Alan Pardew said the player would not be going to South Africa for the tournament without giving a reason.
Although it emerged that a clause in the contract of Ameobi allowed the English Premier League club to retain his services during the tournament, Eagles coach, Keshi did not drop him from the squad until last weekend.
In accordance with Article 36 Paragraphs 2b) and 5c) of Fifa regulations, if a player is called up, he must be released to play in the final competition organised by Fifa or a confederation and held in a period fixed/set in the calendar. In this event, the period of release shall be 14 days.
The NFF thus has the power to appeal to Fifa to stop the player from representing Newcastle during the period of the competition but the federation has now revealed that it will not toe that line.