IOC President Thomas Bach has warned that AIBA's recognition as boxing's International Federation is in serious jeopardy.
This week, AIBA announced that interim president Gafur Rakhimov would stand unopposed for the permanent post in elections in November.
The IOC has previously expressed its worries over Rakhimov's links to crime in his native Uzbekistan, and warned that boxing could be removed from future Olympic Games.
When asked whether boxing would be part of Tokyo 2020 if the stand-off with AIBA continued, Bach stated, "We have always protected the interests of the athletes, albeit for National Olympic Committees like Russia and Kuwait, for not being sanctioned for misbehaviour for which they are not responsible.
"If there should be further measures against AIBA, then we will also find a way to safeguard the interests of these boxers as much as we can."
Boxing is part of the programme at YOG 2018, but Bach says refereeing in Buenos Aires will be "supervised by an independent authority".
IOC alarmed by suspension
Doubts over boxing's future have increased following Rakhimov's probable ascension to the AIBA presidency and how it came about.
AIBA Executive Committee member Terry Smith is alleged to have misled members about an official letter from IOC chief ethics and compliance officer Paquerette Girard Zappelli requesting that Rakhimov not stand for election.
Executive vice president Franco Falcinelli was then suspended for using the letter to back up his support of another candidate, Kazakhstan's Serik Konakbayev, who failed to received the 20 nominations required to oppose Rakhimov.
Bach said, "If you suspend one member because he has advised his colleagues about the contents of a letter by the IOC compliance officer which has officially been sent to the AIBA with a copy to the administration of AIBA, then it is really difficult to understand why this could be the reason for a suspension.
"We have been made aware of communication within AIBA where some leading people are pretending that all the issues with the IOC - regarding governance, regarding refereeing, regarding finance - have been solved."
Bach also insisted that his stance was not about Rakhimov alone.
"It's this overall picture which leads to these major concerns." - IOC President Thomas Bach on AIBA
Boxing's governance crisis
The sport's amateur governing body came under the spotlight when all 36 referees and judges from Rio 2016 were suspended after a string of controversial decisions.
The IOC stopped making payments to AIBA last December until it resolved its problems with governance and finance.
But Rakhimov's appointment as interim president in January raised further concerns which Bach aired the following month.
Ahead of PyeongChang 2018, Bach admitted, "We are extremely worried about the governance of AIBA. The IOC reserves the right to review the right of boxing on the programme of the Youth Olympic Games Buenos Aires 2018 and the Olympic Games Tokyo 2020."
Dr Wu Ching-kuo, also known as CK Wu, led AIBA for 11 years before stepping down in November 2017.
The 71-year-old was banned for life from the organisation this week for "gross negligence and financial mismanagement", allegations Wu strongly denies.