The IOA announced its elected members in voting held in defiance of the IOC, having declared last week that Abhay Singh Chautala had been elected unopposed as president and Lalit Bhanot as secretary-general.
"The elections were held in accordance with a court order," Bhanot said after the elections. "I offer to resign in case I'm pronounced guilty in an ongoing case (of corruption relating to the 2010 Commonealth Games) against me."
The IOC suspended the IOA on Tuesday for failing to comply with the Olympic Charter and its statutes and for failing to inform the IOC in a timely manner.
The IOC asked the IOA to adhere to its own constitution and not follow a government sports code. But it went ahead with the election process, citing a Delhi High Court order that said the polls should be in line with the code.
The IOC's ethics commission had also advised that tainted officials shouldn't hold administrative posts, but Bhanot was declared elected unopposed despite spending 11 months in jail for corruption cases related to the 2010 Commonwealth Games in New Delhi.
IOC spokesman Mark Adams said the elections mean nothing.
"Those elections are null and void, they won't count," Adams told The Associated Press in Lausanne, Switzerland. "They can go ahead with them but they won't have any validity. We have to regain our confidence that the IOA is acting independent of the government and that the government isn't interfering. At the moment, the IOC is not satisfied that this is the case."
The suspended Indian body will stop receiving IOC funding and its officials will be banned from attending Olympic meetings and events. India's athletes will be barred from competing in Olympic events under their national flag, although the IOC could allow them to do so under the Olympic flag.
The Indian body has been mired in wrangling over the elections to replace Suresh Kalmadi, who was jailed for nine months on corruption charges related to the Commonwealth Games.
Kalmadi, who headed the IOA for 16 years, decided not to seek re-election but had been backing Chautala and Bhanot.
Meanwhile, India's sports ministry said in a statement on Wednesday that it's ready to discuss all issues with the IOC and the IOA, and is hopeful that things would be sorted out.
"The IOA had agreed to amend its constitution in 2010 but has failed to bring about the necessary amendments in the past two years," Sports Minister Jitendra Singh said in the statement. "Had this been done, there would have been no cause for intervention by the IOC."
Several Indian athletes hoped the IOC ban would help improve sports administration in the country.
Rifle shooter Abhinav Bindra, India's only individual gold medallist at the Olympics, described the ban as "shameful" for his nation.
"As an athlete, it re-iterates that the athlete is the last person on the agenda in India," Bindra told the NDTV news channel from Munich. "We need professionals running sport in India. At the moment, 100 per cent of their (officials') time is used in working out ways on how they can come to power."
Former athlete Ashwini Nachappa, who is the vice-president of independent body Clean Sports India, which has been fighting for better sports administration in the country, said the IOA had done little for athletes for many years.
"Our athletes have been supported by the government," Nachappa said. "The IOA is not doing anything. The sports ministry is doing everything in terms of ensuring exposure and training for athletes. We hope the system will become better in the coming times."
AP Sports Writer Stephen Wilson in Lausanne, Switzerland, contributed to this report.