International Association of Athletics Federations (IAAF) President Sebastian Coe believes they have a "responsibility to protect" female athletes, following the ruling preventing Caster Semenya from competing at the World Championships in Doha.
The South African will not defend her 800 metres title after the Swiss Supreme Court reversed a ruling which suspended a regulation imposed by the IAAF regarding testosterone levels, pending an appeal from Semenya.
The 28-year-old is appealing a ruling by the Court of Arbitration for Sport (CAS) supporting the IAAF regulation that athletes with differences in sexual development (DSD) who wish to compete in events ranging from 400m and a mile must take medication in order to reduce testosterone levels.
Coe claimed that, while the landscape of sport may change in the future, he feels the IAAF need to maintain a clear division between male and female classifications.
"The importance of trying to keep the sport together, particularly women's sport, that's important to me," Coe told CNN World Sport.
"It may be in 30 years, 40 years time society takes a different view and we have other classifications, I don't know.
"But at this point my responsibility was to protect two classifications and that's what we feel we've done."
Coe insisted the matter is not personal between himself, the IAAF and Semenya, and that he has not spoken to her about the ruling.
"I think it's been handled as sensitively as it possibly could be," he said.
"This is not about an individual athlete, it's not about a particular country, it's not about a continent, and I don't see this as a personal issue.
"I see this as the right decision and those regulations have been tabled for what I believe are the right reasons and, most importantly, the majority of my Council."
Coe reaffirmed his belief that the IAAF decision is correct, claiming the organisation has been "brave" to make an "unpopular" choice.
Referring to Semenya's gender identity as a "condition", he wants the double Olympic gold medallist to return to athletics.
"I hope that she does come back onto the track and I do hope that the athletes with that condition take the medical direction that allows them to do that," he said.
"Look, no Federation, very few big organisations wanted to take the lead role in the challenges around DSD, and clearly, these inspire societal discussions as well.
"Transgender is, you know, is going to be a massive issue, not just for athletics but for so many other sports.
"I want athletics to always be at the forefront of thought leadership.
"I'm happy that our sport is brave enough to want to challenge these issues and take them head on.
"And that doesn't always leave you in popular positions, but they do tend to be the right positions to be in."
Three-times world champion Semenya has accused the IAAF of using her as a "guinea pig" as part of an extended war of words with the worldwide governing body.
She has also warned she will "not allow the IAAF to use me and my body again".
The IAAF World Athletics Championships are due to take place from September 27 to October 6 at Khalifa International Stadium.