The outspoken former winger believes the club's current struggles are the result of long-standing issues rather than a sudden downturn in results.
"Kaizer Chiefs' problems didn't start yesterday, but have been ongoing for some time," Khanye said, as quoted by Soccer Laduma.
He pointed to previous coaching eras as a turning point, arguing that the team's identity and style of play were gradually lost over the years.
"Since the club had the likes of Giovanni Solinas, Ernst Middendorp and Stuart Baxter coaching the team, back in those days, the team's style of play got affected big time."
Khanye believes a series of poor decisions - particularly in the recruitment of both coaches and players - has left the club struggling to compete at the level expected of South Africa's most decorated side.
"The situation we are seeing now at Chiefs is a result of a number of factors, with wrong decisions having been made on both coaches and the players that are being brought to the club," he said.
The former attacker was also critical of the quality within the current squad, suggesting many players are not meeting the standards required at Naturena.
"You can argue with me all you want, but you can't tell me that players who finish a game against Richards Bay FC without a single shot on target are good enough to play for a club as big as Chiefs," he said.
Khanye also highlighted their struggles in big matches, referencing their recent clash with arch-rivals Orlando Pirates.
"You go for an entire first half against your rivals Orlando Pirates without having a corner kick, and you want to tell me that you are good enough to play for Chiefs? No, never."
He compared the current squad with the team he played in alongside stars such as Tinashe Nengomasha, Patrick Mabedi and Collins Mbesuma.
With Chiefs now battling to remain in the Top Eight, Khanye warned that their place in the upper half of the table is far from secure.
Amakhosi will look to steady their campaign when they host Durban City at FNB Stadium on March 15 in a match that could prove crucial in their push for a Top Eight finish.