The athletes, who were part of a 27-member track and field squad, were barred from taking part in the Games because they were above the stipulated age of 17, an official said.
"It should not have happened. We are trying to find out the reason," the Indian Olympic Association's interim chief Vijay Kumar Malhotra told reporters in New Delhi.
Two days ago, four Indian badminton players were prevented from competing in Nanjing because organisers said their names had not been entered for the competition by officials back home.
India has been suspended from the Olympic movement by the International Olympic Committee (IOC) since December last year for electing corruption-tainted officials to its local association.
The country's young sports stars are taking part in the Nanjing Games as "independent" Olympic athletes under the IOC flag.
They were selected by the Athletics Federation of India (AFI) and approved by the state-run Sports Authority of India (SAI).
Athletics officials would not comment on the over-age problems, but SAI chief Jiji Thomson blamed the AFI for the mix-up.
"When a federation gives us a list, we never question it," Thomson told the Times of India. "It's entirely the responsibility of the federation to pick a team and ensure everything is in order."