Speaking in Pyeongchang ahead of next week's Winter Olympics, Bach said the IOC was "extremely worried" about how the sport was run and said the body was prepared to make bold decisions.
"The IOC reserves the right to review the inclusion of boxing in the programs of the Youth Olympics 2018 and Tokyo 2020," he told reporters.
Bach added that the IOC would be freezing all contacts with the sport's governing AIBA "excluding the ones on a working level necessary to implement the respective IOC decisions".
AIBA said the IOC decision was "extremely disappointing" after the boxing body had submitted a progress report as requested.
Following a two-day Executive Board meeting in Pyeongchang, Bach said the IOC had not been satisfied with the AIBA report and that it would be opening an investigation into the body.
AIBA has been riven with in-fighting for months, with former president and IOC member CK Wu first provisionally suspended and then stepping down last November after a bitter dispute with his executive committee.
AIBA named Uzbek Gafur Rahimov as its new Interim President last Saturday, following the unexpected resignation of Interim President Franco Falcinelli.
The Olympic ruling body had also announced in December it was freezing payments to AIBA until boxing got its house in order.
Previously, the IOC withheld payment of more than $1 million of television rights from the Athens 2004 Olympics after a refereeing scandal at those Games.
AIBA said in a statement that the IOC had demanded a new report on its governance by April 30th and it would comply with that.
"This decision was made despite AIBA’s fulfilment of the IOC’s request to submit a Progress Report outlining all steps AIBA was asked to take and continues to take to improve its governance," it added.
The statement said AIBA had hoped the IOC would have understood that "the processes necessary to implement even more measures require more time."
The boxing body added that it had shown already a willingness to reform and would be carrying out a complete organisational review over the next six months leading to a "New Foundation Plan".
The Winter Olympics runs from Feb. 9-25.
(Additional reporting by Alan Baldwin in London, editing by Toby Davis)
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