Both the International Judo Federation (IJF) and Kelmendi's coach confirmed on Monday that the 25-year-old had refused to take an out-of-competition drugs test while training in St Cyprien in France on July 16.
The IFJ said: "A control was done in June in France. The procedure is contested by the athlete and her coach and looks questionable at the level of the IJF."
However, it added that any sanction given would apply only in French territory.
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Kelmendi's coach, Agron Kuka, insisted the test had been refused due to a perceived lack of authority by the person administering it, rather than because of any use of banned-substances.
Speaking to the Guardian, Kuka said: "The team was in the training camp in France and some person came and asked to do the doping control. But the person involved, she didn’t have any authorisation from WADA [the World Anti Doping Agency] or anyone. And that’s the end of the story.
"Then afterwards [the French] made a complaint somewhere and were trying to take the case to court or something... The Kosovan team were in discussion with the IJF the whole time because they are not going to go and give the blood or the urine to somebody who is not responsible. That is the end of the story, it’s nothing else.”
He added: "I don’t know the reason why they are making a big deal out of it. It’s nonsense.”
The incident potentially casts a shadow over Kelmendi's gold medal victory in the women's -52kg Judo event on Sunday, which was also Kosovo's first Olympic medal with the country represented for the first time at the Rio Olympics.
Kelmendi previously represented Albania at the 2012 Olympics in London, prior to the IOC's official recognition of Kosovo in 2014, exiting in the second round.
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