The Athletics Federation of India was warned by the government on Tuesday to hold re-elections for key posts or face suspension.
The sports ministry, which won't recognise the Indian Amateur Boxing Federation and the Archery Association of India for not following a government sports code during their recent elections, announced in a press release the AFI's "recognition shall stand withdrawn without any further notice" if it did not amend its constitution and hold fresh polls for the posts of president, secretary and treasurer.
The objections were in respect to AFI rules which allow only previous executive members to become president or secretary as well as a condition that a candidate's name needs to be proposed by three members rather than one.
Indian sports federations have come under scrutiny from the government and the International Olympic Committee in recent days.
On Friday, the government withdrew its recognition of the IABF within hours of its suspension by world body AIBA for not following proper electoral procedures.
It also withheld support of the AAI for failing to follow age and tenure restrictions in the sports code.
The latest government announcement has come within four days of the IOC suspending the Indian Olympic Association because of government interference in its election process.
Abhay Singh Chautala became president of the IOA in elections which were declared "null and void" by the world body. He was also the chairman of the IABF before its suspension.
Tainted official Lalit Bhanot, who was in jail along with Suresh Kalmadi for corruption cases related to the organisation of the 2010 Commonwealth Games in New Delhi, had been elected secretary general of the IOA.
Both Chautala and Bhanot were said to be backed by Kalmadi in the IOA elections.
Kalmadi also wields considerable power in the AFI, of which he is a past president.