Hoy rejected the claim, saying he would not have achieved such success without the help and support of Team GB, and rower and fellow Olympic medallist Katherine Grainger also distanced herself from such talk.
Chris Adcock and Imogen Bankier say the sport's programme 'does work'
Hunt added: "Last year at the 2011 badminton World Championships, Chris Adcock and Imogen Bankier, who are an English and Scottish pairing, won a silver medal - this wouldn't have been possible if we weren't working together.
"They are a real medal prospect in London 2012 - so there's no doubt that together we are much stronger."
Hunt, who was speaking at the Winter Youth Olympic Games in Innsbruck, Austria, added that Glasgow is a potentially strong candidate city to host the 2018 summer Youth Olympics, should the BOA decide to bid.
"We're out there evaluating cities at the moment," Hunt told BBC Sport.
"We've had really good interest from Glasgow and that would be a brilliant legacy from the 2014 Commonwealth Games, so I think it's really interesting.
"We'll wait to see what the submissions are like, evaluate to see all the guarantees and commitments needed for the bid are there, because if we are going to be in it, we want to win it - and we wouldn't be doing it otherwise."
Jade Jones wins Britain's first gold at the 2010 Youth Olympic Games
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