The IABF, which was terminated by the International Boxing Association (AIBA) in 2014 before being de-recognised by the sports ministry, had conducted a meeting last month, inviting state units to revive their membership.
This despite the fact that the Boxing Federation of India (BFI), which was elected to office last year, is the recognised body to run the sport in the country.
"As of now, IABF is not having the recognition of the international body i.e. AIBA...only the recognised National Sports Federation is entitled to use the expression of 'India' or 'Indian' in its title or in any athletic competition controlled by it..." the ministry letter stated.
The IABF was terminated by the AIBA for manipulation in its 2012 elections, a move that led to four years of administrative turmoil in Indian boxing.
Fresh signs of turbulence emerged after the IABF meeting last month, in which the BFI affiliated Haryana state association was represented by its Secretary General Rakesh Thakran.
Thakran has been issued a show cause notice by the BFI.