The audits will begin in 2016 and will apply to all international federations which receive financial aid from the IOC.
"The audits will be led by independent organisations," said Bach, and will also include national Olympic committees and Olympic Games organising committees.
The move comes as world football's governing body FIFA and the IAAF, which controls track and field, are mired in corruption scandals.
On the ongoing FIFA crisis, Bach said he was encouraged by a range of reforms which should be adopted by the body's 209 federations next February when a new president to succeed the suspended Sepp Blatter will be elected.
"So yes I think these reforms when they have been approved by the Congress are a basis."
However, in a later statement, the IOC added that they were concerned over the lengthy nature of the twin investigations being carried out by the US and Swiss judicial authorities into FIFA corruption.
"The IOC executive board welcomed the proposals by the FIFA Executive Committee for major reforms like term limits and other measures," said the statement.
"Since this could continue to overshadow the credibility of FIFA and affect all sport organisations for such a long time, the IOC executive board encourages FIFA to take all necessary measures to clarify and resolve all the pending issues as soon as possible by further engaging with the relevant authorities.
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