Tuesday, the IOC banned the Indian Olympic Association (IOA) and said a vote to elect its secretary-general on Wednesday would be "null and void".
Lalit Bhanot, who spent 11 months in custody last year following corruption charges that plagued the 2010 Commonwealth Games in Delhi and who is out on bail, was left as the only candidate for the post after his rivals pulled out.
The ban means an effective end to funding from the IOC, no Indian officials attending Olympic meetings and Indian athletes banned from competing at the Olympics under their country's flag.
"This is unfortunate. As a sportsperson, I feel like I have been orphaned," shooter Joydeep Karmakar told Reuters.
"It's a big blow to us. I think the IOC is going to suspend funding and there could be other repercussions as well," added Karmakar, who just missed out on a bronze medal in the men's 50m rifle prone at the London Olympics.
"Playing under the national flag means a lot for us. Competing under the Olympic flag won't give you the same feeling.
"At the same time, I'm optimistic it would lead to a new body which would be more efficient and more responsible."
Former double trap shooter Moraad Ali Khan echoed Karmakar's sentiments.
"Standing on the podium with the national anthem being played and the nation's flag unfurled, it's a different feeling altogether and it has been taken away from Indian athletes," Khan told Reuters.
"But when medicine doesn't work, what do you do? You go for surgery and we had reached that stage."
Khan, who won gold at the 2002 Manchester Commonwealth Games in men's double trap pair, said it seemed like the IOC's move was the last resort.
"Only a drastic step like this could have shaken the ailing system. It's time for taking the corrective measures. Maybe you won't see overnight changes but I expect some positive developments in the coming months."
Shooter Abhinav Bindra, who won India's first individual Olympic gold at the 2008 Beijing Games, was also left hoping the ban could bring about a better governing body to run sports in the world's second most populous nation.
Bindra is one of the few Indian athletes to consistently question India's sports administrators.
"Bye Bye IOA, hope to see u again soon, hopefully cleaner!" he said on his Twitter feed.
The IOC's move to ban the Indian body, which has been plagued by in-fighting and criticised for lacking transparency, also found favour outside India's sporting community.
Best-selling Indian author Chetan Bhagat suggested even more drastic measures were in order.
"As an Indian, I am happy that the IOA has been suspended. Some of our authorities change only when thoroughly shamed," he Tweeted.
"Dear IOC, you have suspended the IOA. Now if only you could round up the officials, take a javelin and ... oh well, one step at a time."