Nigeria's loss in Egypt ruled them out of contention for Gabon 2017, leaving Kanu upset with the NFF.
"What is happening with Nigerian football is that the top management is not what it is supposed to be so what is below is being affected," Kanu told BBC Sport exclusively from Uganda.
Ex-Arsenal forward Kanu was in Uganda as an ambassador for both Unicef and Chinese cable station TV StarTimes, helping to market Ugandan players to the Chinese Premier League.
He said the Nigeria Federation has to change its style of leadership if Nigeria are to achieve success.
"When the head is not right, even your body won't be right", said Kanu.
The two time African footballer of the year said it was a huge loss for Nigeria - who also failed to qualify for Equatorial Guinea in 2015 - to miss another Africa Cup of Nations.
"When we are not at the Nations Cup, it's not the same," said Kanu.
Kanu also highlighted the instability surrounding Nigeria coaches.
Samson Siasia was placed in temporary charge of the Super Eagles for the Egypt qualifiers following the resignation of Sunday Oliseh.
As the NFF search for a permanent successor to Oliseh, Kanu maintained it is worth persisting with a local coach.
"Look at Stephen Keshi, he won the nations Cup and led the Super Eagles to the last 16 at the 2014 World Cup in Brazil," Kanu explained.
During his time in Uganda, Kanu had the opportunity to play football with children in Katanga, and saw some local matches.
"I watched a game between KCCA FC and SC Villa in the 2016 Star Times Cup a few days ago and I saw a lot of talent that can go to the professional level."
Former Super Eagles captain Nwankwo Kanu has criticised the Nigeria Football Federation's (NFF) leadership which he says contributed to the national team failing to qualify for two consecutive Africa Cup of Nations.