The Swiss Federal Tribunal (SFT) ruled Semenya will be able to run in her favoured 800 metres event without taking medication until her appeal has been ruled on.
In response to that decision the IAAF said in a statement that it would seek a "swift reversion of the superprovisional order... to avoid serious confusion amongst athletes and event organisers and to protect the integrity of the sport."
It added that the suspension of regulations applied only to Semenya and will be in effect until June 25.
"The SFT's decision was "ex parte", meaning that it was requested and issued without the IAAF’s knowledge," athletics' governing body said.
"The IAAF did not receive appellant’s filings or the order until today so has not had the chance to explain why the DSD Regulations should remain in force and applicable to all affected athletes while the appeal is pending."
Reuters has contacted Semenya's representatives for comment.
In defence of its rules, the IAAF said it was committed to the full participation of women in athletics and would continue to fight for equal rights and opportunities for all women.
"The IAAF fully respects each individual's personal dignity and supports the social movement to have people accepted in society based on their chosen legal sex and/or gender identity," the IAAF statement added.
"However, the IAAF is convinced there are some contexts, sport being one of them, where biology has to trump identity.
"The IAAF also believes the right to participate in sport does not translate to a right to self-identify into a competition category or an event."
(Reporting by Nick Said; Editing by Toby Davis)
