Ngeny, who quit last weekend as AK athletes' representative, said too much money was going towards funding the travel and expenses of officials instead of developing athletics.
Kenya is a global leader in endurance running on the track and in city marathons but more than 40 of its athletes have been banned for doping in the past three years.
Four senior AK officials have also been suspended for misusing funds amid other allegations.
Ngeny said he was annoyed Kenya was sending six officials to the United States for this month's world indoor games in Portland, Oregon along to accompany 11 athletes.
He added that five Kenyan officials will be sent to Cardiff for the world half-marathon in March with 10 athletes.
"If you see such kind of composition, it shows... the AK is not really serious," Ngeny told Reuters in Kenya's capital Nairobi. "It’s really worrying."
AK could not immediately be reached for comment.
OFFICIALS SUSPENDED
Former AK president Isaiah Kiplagat, his former deputy David Okeyo, and former AK treasurer Joseph Kinyua have all been suspended by the IAAF Ethics Commission on charges of misusing funds from a sponsorship by U.S. sports manufacturer Nike.
Last month AK chief executive Isaac Mwangi was also provisionally suspended by the Ethics Board of the sport's world governing body after being accused of seeking bribes to reduce doping suspensions of two athletes.
All the officials deny any wrongdoing but the bans, coupled with the slew of failed drug tests, have cast a shadow over Kenya's preparation for this year's Rio de Janeiro Olympics.
The World Anti-Doping Agency (WADA) has given Kenya until April 5 to prove it can successfully tackle the doping issue, or face exclusion from the Games.
Ngeny said AK needs to fundamentally change, and called for new elections at the federation to install fresh management.
"We have failed as a federation," he said. "This is a right time now for AK, the whole executive, to step aside. Then we will have new blood in the system."
(Reporting by Drazen Jorgic; Editing by George Obulutsa and Ken Ferris)
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