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The IOC had warned AIBA in February to sort out its finances, the sport's governance and anti-doping issues but a progress report presented this week was insufficient, IOC president Thomas Bach said on Thursday.
"This report shows some progress and shows goodwill but still lacks execution and in some areas lacks substance," the German former Olympic fencer said.
"So our concerns on governance, financial and sporting integrity are continuing and we think that we need to see action on the plans."
AIBA has been riven with in-fighting for months, with former president CK Wu first provisionally suspended and then stepping down last November after a bitter dispute with his own executive committee.
AIBA then named Uzbek Gafur Rahimov as its new interim president following the unexpected resignation of previous interim chief Franco Falcinelli.
Bach did not refer to the new leadership but said the slow pace of chances could affect boxing's chances to make it to Tokyo 2020. He also said boxing would urgently need to review the way judges are appointed for matches.
"Therefore we retain our right to exclude boxing from the programme of the Tokyo 2020 Olympic Games," Bach added.
The IOC has already frozen any payments to the association though it is not the first time AIBA has had IOC funds blocked.
The Olympic ruling body withheld payments of more than $1 million of television rights from the Athens 2004 Olympics after a refereeing scandal at those Games.
"The whole AIBA organisation has been working extremely hard in the last few months," Tom Virgets, AIBA Executive Director said in a statement.
"In line with our commitment to transparency, we look forward to sharing the submitted report with all of our members as soon as possible. This is a new AIBA and we are fully committed to putting into action the values of Boxing and the Olympic Movement."