The IOC recommended last month that boxing should keep its place at next year's Games but recognition of AIBA, the governing body of the sport's amateur version, should be suspended until the issues surrounding its finances and governance are resolved.
AIBA has been in turmoil over its finances and governance for years with the federation $16 million in debt and an ongoing bitter battle over the presidency that has split the body internally.
The IOC has since set up a task force to look into the structure of the qualification and the Olympic competition amid growing concern from boxers.
"I do not think we can really compare the AIBA situation to any other international federations," Bach told a conference call.
"The AIBA issues are many fold, an aggregation of challenges and we cannot see this in any other international federation. I hope it will stay like this so that the AIBA situation will remain a unique experience."
While the IOC organises the Olympic Games as a whole, the federations run their own sports competitions within that framework.
Bach said the IOC executive board and session in Lausanne next week will hear the task force's proposals for the qualification process and the structure of the organisation running the boxing competition in Tokyo.
"So that athletes know what they have to expect (on the road to Tokyo)," Bach said.
Other international federations are struggling with different issues, such as doping in weightlifting (IWF), governance and control of competitions in swimming (FINA) and basketball (FIBA) among others.
On the marketing front, German athletes scored a big court win in February to earn more rights from the IOC for promotional activities ahead of and during the Olympic Games.
Revenues from the Olympic Games are the main source of income for several of the smaller federations.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar)
