"Unfortunately, it's a fact that it has damaged our image. I've heard lots of people wonder how such things can happen in Switzerland," Peter Gillieron told the Swiss federation (SFV) website.
"With both FIFA and the International Olympic Committee having their headquarters in Switzerland, sport in general, not just football, is in danger if the rules of the federations are undone by appeals to civil courts."
Sion were thrown out of the Europa League by football's European governing body UEFA for fielding ineligible players in their play-off tie against Celtic.
The players in question were signed in the close season despite the club being subject to a transfer ban imposed by football's world governing body FIFA after Sion were judged to have incited an Egyptian goalkeeper to break an existing contract to join them in 2008.
Sion's outspoken president Christian Constantin has taken the case to a civil court in Vaud, the canton where UEFA's headquarters its based, and won a "superprovisional" order ruling that his team should be reinstated.
UEFA has not accepted the ruling and Celtic have taken Sion's place in the Europa League group stage.
Sion had also used a civil court to overturn a ban on the players being allowed to play in Switzerland, a ruling which was accepted by the Swiss League.
"It is recognised that it is difficult for us when civil courts make decisions which contradict those made by UEFA, but have to be carried out under Swiss law," said Gillieron.
"I believe UEFA's measures to be correct," he said. "The continuous appeals to civil courts or a letter addressed to the Federal Council, asking for an intervention in UEFA and FIFA, are damaging for sport and for FIFA."
"For my part, I ask if it is acceptable to put in danger Switzerland's reputation in relation to the world of sport, because Sion have made a non-authorised transfer and its president has rebelled instead of accepting and respecting the sentence against them."
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