The Indian Amateur Boxing Federation was suspended in late 2012 for 'possible manipulation' in its elections and eventually terminated by AIBA in March this year.
AIBA subsequently gave provisional approval to a new group called Boxing India which ignored bickering units and held fresh elections last week.
"I would like first of all to congratulate you and your new national federation on the recent elections of all the executive of Boxing India including you as its president," AIBA chief Ching-Kuo Wu wrote in a letter to Boxing India president Sandeep Jajodia.
"I would like to emphasise the importance of managing Boxing India in the most transparent, fair, democratic manner and most importantly in the respect of all AIBA rules and regulations."
The AIBA also advised the new body to seek recognition from the Indian Olympic Association in the near future.
The Indian boxers contributed nine medals, including two gold medals, at the last Asian Games in Guangzhou - their second highest in all disciplines.
But leading boxer Vijender Singh will be unable to defend his Asian Games middleweight title after a hand injury ruled him out of the Incheon Games, which kick off with the opening ceremony on Friday.
(Reporting by Sudipto Ganguly; editing by Patrick Johnston)
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