Gian Franco Kasper, an International Olympic Committee executive board member, said he was "truly sorry" for his comments to journalists in Pyeongchang, South Korea.
"It was an inappropriate and insensitive comment," the 73-year-old Swiss, head of the world winter sports body, said in a statement.
"I apologise unreservedly for any offence I have caused. I am truly sorry."
Kasper made his controversial remarks earlier on Thursday when asked about the prospect of barring Russia from next year's Winter Olympics in Pyeongchang over its doping record.
"I'm just against bans or sanctioning of innocent people," Kasper said, on the sidelines of an IOC executive board meeting in Pyeongchang.
"Like Mr. Hitler did -- all Jews were to be killed, independently of what they did or did not."
When challenged about comparing the two situations, Kasper said: "Why not? Of course it's more extreme. But just the fact that the place you come from makes you guilty, I'm not okay for this, really not."
He formerly sat on WADA's executive committee, and has been an IOC member since 2000.
Kasper was speaking as the IOC executive board deliberated proposals for the reform of WADA following calls for a shake-up in the fight against doping.
The IOC came under fire last year when it stopped short of banning Russia outright from the Rio Olympics, and instead let individual sports federations decide which Russian athletes could compete.
"I'm fully against banning or punishing somebody because of his passport," Kasper said.
"It's... The same (thing). We are here to protect the clean athlete, not punish the clean athlete."
Among the revelations of WADA's McLaren report were that Russia used a "mouse hole" in the wall of its Sochi laboratory to swap tainted urine samples with clean ones overnight.
WADA chief Craig Reedie warned this week that Russia still had "significant work" to do before the suspension of its anti-doping body, RUSADA, is lifted.
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