"What we want to achieve is that this money which is coming from sport is going to sport and that the decisions on who is benefiting at the end from these contributions are being taken with respect to rules of good governance," Bach told reporters at the end of an IOC Executive Board meeting.
The IOC, concerned with the ongoing scandals engulfing soccer's world governing body FIFA and the international athletics federation (IAAF), is eager to make sure major payments to international sports federations, national Olympic Committees (NOCs) and Games organising committees is accountable.
Bach said the auditing would be conducted by an independent organisation and would start for the year 2016 for every major contribution by the IOC.
He said the move was a further step by the IOC to boost good governance for both the organisation and its partners.
FIFA and the IAAF are facing investigations of corruption involving senior officials, with the crisis eroding the organisations' credibility.
Several senior FIFA officials are among the 41 people arrested in connection to a corruption and racketeering probe while the former head of the IAAF Lamine Diack is also under formal investigation in France for allegations of corruption and money-laundering.
With athletics and soccer both Olympic sports they are eligible for Olympic contributions at the end of each Games. About $519 million (£342 million) was distributed among the 26 sports after the London 2012 Games.
Games organisers receive well over one billion dollars from the IOC to help organise the Games while NOCs receive further funds.
Bach said ongoing scandals at FIFA were damaging for all sports organisations, even those not involved in scandals.
"I think it is obvious many sports organisations are concerned because many people do not make this distinction. They generalise," Bach said.
"That is why we are concerned and why so many other sports organisations are concerned and continue to be concerned if these procedures are dragging on and on and you have from week to week other bad news coming up."
(Reporting by Karolos Grohmann; editing by Martyn Herman)
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