It was unclear whether the decision, involving an episode that originally aired in the United States in 2005, was made by channel executives or regulators. Channel executives could not be reached for comment Friday.
A spokesman with Russia's broadcast regulator, Rosskomnadzor, said he knew nothing of the incident.
"We have never interfered with editorial decisions," Yevgeny Strelchik said.
The channel has been threatened with closure at least twice before for broadcasting what material regulators deem extremist. The network received warnings from the government last year for "promoting immorality and violence" and again in September 2008 for "overt propaganda of homosexuality and pedophilia."
Religious groups have also sought to have the station's license revoked.
The Soviet collapse loosened the reins on news and information, and open mocking of government officials - Kremlin or otherwise - was popular in the 1990s. Under Putin's presidency, however, there's been a noticeable shift away from biting satire.
The channel NTV was forced to pull its satirical puppet show "Kukly" in 2002 after the Kremlin objected to the excessive lampooning of Putin.
Putin, who is now prime minister, has been instrumental in returning economic stability to Russia but critics say that his methods, which leave little room for public dissent, border on authoritarian.
Internet publications and blogs are among the last outlets for unfettered commentary and satire in Russian, and commentators on Russia's most popular blogging service, Live Journal, vented their anger after news of the "South Park" censorship leaked out.
"Congratulations, Vladimir Vladimirovich," wrote one blogger, manhater-1138, referring to Putin by his name and his patryonimc. "You have become pornography."
Oleg Kuvaev, a blogger and online animated filmmaker, said on his Web site that the decision would only attract more attention to the channel.
"It's stupid to cut things this way, because the result is reverse - a mediocre scene attracts more interest," he wrote.
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