Bhupathi and Bopanna had defied AITA's decision of asking them to play with Leander Paes for the 2012 London Games. They refused to play with Paes to play together at the Games.
The AITA was quick to react against the charges, saying Bhupathi was free to take legal recourse against the association.
Bhupathi accused AITA president Anil Khanna of taking the advantage of his rift with Paes. Bhupathi also said that he would "explore legal options" against the AITA.
Bhupathi in his scathing attack on the AITA said its administration is detrimental to growth of sport in the country and he has no choice but to accept the two-year ban slapped on him by the "dictatorial" body.
Hiranmoy Chatterjee, senior executive committee member of the AITA, said that the association was justified in sidelining Bhupathi and Rohan Bopanna from playing in the national team till June 2014.
"The AITA is not perturbed by Bhupathi's threat of a legal action. We have gone by the rule book. The decision was taken by the ethics committee according to rule 36 (A2) of our constitution," Chatterjee told IANS over phone from Kolkata.
Chatterjee said Bhupathi "wants to be a selector, player and an administrator at the same time."
"He selects himself and then decides with whom to play. If he has to do everything then what is the selection committee there for. We have sent out a strong signal that indiscipline will not be tolerated," said Chatterjee.
"Mahesh is now saying he doesn't know where to complain. But he was well aware where to voice is displeasure when he was asked to play with Paes during the Games," he added.
Bhupathi, 38, who is at the fag-end of his career, said that after much thought he decided to take on the AITA.
"I am here to detail episodes of the personal vendetta the AITA and its dictatorial rule have carried out against me over the last decade. Tennis has given me everything I am today and, by god's grace, I am able to give back a lot to my sport, be it running tennis events, building tennis courts, raising money for talented kids and even opening academies across the country," Bhupathi read out his statement at a media conference here.
"However, at every step of the way the establishment has put a spoke in the wheel. So much so that they changed the constitution to make sure we are not able to run any event in India without them being part of it."
Taking a dig at AITA president Anil Khanna, Bhupathi said Khanna enjoyed the public spat between him and Paes.
"Anil Khanna has enjoyed the rift between Leander and me as no other. He has re-defined the term divide and rule and at this year's Olympics, used Leander's shoulder to fire the gun against me multiple times. Unfortunately, the media terms this a Bhupathi-Paes rift and the true underbelly is left unquestioned."
The 37-year-old claimed that AITA was jealous of the fact that he has been able to do more for the sport.
"Over 80 percent of members of the executive committee have sat there for close to twenty years if not more and they are yet to produce one professional tennis player. The Krishnans, the Amritrajs, Zeeshan (Ali), Leander, Sania (Mirza), Rohan (Bopanna), Somdev (Devvarman) and Yuki (Bhambri) have not benefited from their system. Yet they continue to hold their positions and go about their jobs in the name of Indian tennis.''
"I have extended a hand of friendship to Anil Khanna several times but he was not forthcoming. He always wanted full control of things."
Bhupathi said he felt for his partner and regretted not playing his farewell match for India.
"It looks like I have no choice but to accept this ban. I don't know who to complain on the matter.
"I do feel really bad for my friend and partner Rohan who has been caught in the cross-fire of dirty politics. As far as I'm concerned I was always banned by the AITA, they never supported anything I did for the sport, only when they couldn't do without me and they needed the doubles point in Davis Cup, I got the E-mail.
"They continue to misuse the power. They have to try and teach me a lesson only because they feel I am able to do a lot more for the sport than they do," he concluded.