"Most of the South Africans playing in the IPL are performing very well," Ntini told the daily Business Day.
"Perhaps that's because they are playing in different teams and not together. Our players tend to perform better as individuals compared to a team. That's often their downfall and it's something I don't understand," he added.
Ntini's comments came in the wake of fine performances by Morne Morkel, Dale Steyn and Jacques Kallis who are among the top 12 wicket-takers in the IPL. Batsmen Faf du Plessis and AB de Villiers were among the top 15 run scorers.
"When the guys play in the IPL or in our own provincial sides they perform excellently and that should also go for when they're playing for the country," Ntini told the daily.
"But when they are together they don't peak as a team in the same way as they do when they are playing as individuals for other sides and obviously we need the guys who are playing well now to also do so for South Africa."