The elections were held amid speculations that tainted former AFI Secretary Lalit Bhanot dictated terms to maintain his hold in the federation.
Bhanot, who was released on bail in connection with the Commonwealth Games scandal, attended the AGM as a delegate of Delhi Athletics Association.
Maharashtra Athletics Association chief Adille Sumariwalla was elected unopposed as president while C K Valson was made Secretary in the absence of any opposition candidate in the AGM.
Unlike last year, media was barred from the AGM.
With Sumariwalla taking over as AFI chief, it is for the first time that an Olympian and Arjuna awardee would be at the helm of affairs.
Valson is an ex-athlete and technical official in many international events, including Guangzhou Asian Games. He was the competition manager of athletics in the 2010 Commonwealth Games.
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Karnataka Athletics Association secretary Satyanarayan was elected unopposed as Treasurer.
Retired Delhi High Court Judge Justice J D Kapoor was the returning officer of the polls while S K Mendiratta, the legal advisor in the Planning Commission, and Roque Dias from the Sports Authority of India were the government observers who oversaw the elections.
According to an AFI release, Justice Kapoor appreciated the election process and informed the members that the polls have been conducted transparently and as per AFI Constitution.
"The President, Secretary and Treasurer have all been elected for the first time," the release said.