The ministry has asked the tennis body to elect a new President within 90 days. The post has been lying vacant ever since Anil Khanna refused a second term despite being elected.
Khanna had refused the position at AITA's AGM in Indore citing ambiguity on the issue of cooling off period. The veteran administrator had been elected President after serving successive terms as Secretary General.
The Federation installed the him as Life President and elected other office bearers at the meeting on September 3.
The government deems Khanna's first Presidential term against the rules under Sports Code but the tennis body contends it has not flouted any rule.
"I will call an SGM and conduct elections for the post of President but first the government must give us the guidelines as to which amendments we need to carry out? We were the first Federation to follow the Sports Code, the age and tenure guidelines," AITA Secretary General Hironmoy Chatterjee told PTI and added they have written to the ministry on the issue asking for clarity.
"If Mr Khanna is not eligible, he's not eligible, but nowhere the rules say that the President has to serve a cooling off period. It's only for the Secretary General and Treasurer. The government guidelines are not clear. They must clarify first and it has to be same for everyone. They can't single us out," Chatterjee said further.
The AITA official also argued that they are following the same guidelines, which the IOA adopted before being granted recognition.
"We are willing to incorporate the changes but it has to be uniform. We don't want any confrontation with the government, we want to work together."
ITF, the world governing body for tennis, allows three consecutive terms as President.
Khanna was elected as AITA president for a four-year term (2012-2016) after serving as Secretary General for two consecutive terms.
The Sports Code requires a cooling off period of four years if an office-bearer seeks re-election after serving two consecutive terms.
AITA contends that Khanna did not seek re-election as Secretary General but was elected as President in June 2012 and there were no instructions that a person, who has served as secretary general, cannot become president without serving cooling-off period.
Khanna had narrowly lost the ITF presidential elections but was elected as Vice-President of the world governing body of the sport and was also included in the powerful board of directors.
After becoming ITF Vice President, Khanna had offered to step down as AITA President last year but the Executive Committee stopped him.