The Algerian, 25, won women’s welterweight gold in Paris at the Paris Olympics, a year after being disqualified from the World Championships for reportedly failing gender eligibility tests.
The tests were conducted by the Russian-led IBA, who were later stripped of their world governing body status by the IOC over integrity and governance issues.
At the time the IBA said Khelif “failed to meet the eligibility criteria for participating in women’s competition”.
The IOC questioned the legitimacy and credibility of the IBA’s tests, saying they could not be relied upon.
The IOC was responsible for running the boxing competition at the Paris Olympics.
Khelif and Taiwan’s Lin Yu-ting, who was also banned by the IBA, were both cleared to compete at the Olympics by the IOC.
The pair’s gold medals overshadowed boxing at Paris and attracted scrutiny and criticism from around the world.
Khelif said her team was now reviewing the situation and would take legal action to protect her rights.
The IOC has said the IBA statement was “just another example of the IBA’s campaign against the IOC”.
Switzerland’s Attorney General’s office confirmed it had received the IBA’s complaint.