VKontakte (www.vk.com), Europe's largest homegrown social network with 210 million registered users, was put overnight on a "black list" of sites barred from distributing content inside Russia. Hours later, the ban was lifted.
The company's founder Pavel Durov has clashed with the authorities in the past for providing a forum for opposition activists to organise protests against Putin.
"This happened by mistake," said Vladimir Pikov, a spokesman for Roskomnadzor, the state communications regulator.
"In this case, someone checked a box against the address of the social network. The site has been removed from the list and restrictions on access to it have been lifted."
Durov, 28, founded VKontakte in his native St Petersburg in 2006 and his success in building the network - which attracts 47 million users daily who log on to share news, views and photos - has drawn comparisons to Facebook's Mark Zuckerberg.
Durov refused to comply with an order by the Federal Security Service, a successor to the Soviet-era KGB, to close groups used by activists to organise protests over the December 2011 parliamentary election, which handed victory to Putin's ruling United Russia party.
Last month, he was implicated in a traffic incident in the city of St Petersburg in which a policeman was slightly injured.
Durov has denied being involved in the accident but, instead of agreeing to testify as a witness, he left the country, say sources who know him. He has not been seen in public or posted on his VKontakte page since April 24.
The executive's difficulties coincided with a change of ownership at the company, in which a private equity fund with Kremlin connections bought a 48 percent stake from the founding partners who backed Durov.
The day before the deal closed on April 17, VK's office and Durov's home were searched by investigators.
The buyer, United Capital Partners, controls assets worth some $3.5 billion and is run by financier Ilya Sherbovich, who sits on the board of three large state firms including Rosneft, the oil major run by Putin's former chief of staff, Igor Sechin.
"It's a meticulous and methodical effort to bring the network under the control of the Kremlin," science fiction writer and blogger Dmitry Glukhovsky, creator of the Metro 2033 video game, told Reuters this week of the pressure on VK.
"It's too important a resource to stand independently from the 'siloviki'," added Glukhovsky, referring to Putin's allies that share the Russian leader's security-service background and are now in the political ascendant.
Sherbovich, in an interview, has denied fronting for the Kremlin and said he wanted Durov to stay on as chief executive of VKontakte.
A source close to the company said it held a board meeting in Switzerland this week which was attended by Durov.
Durov owns 12 percent of VK, but under a shareholder pact he also votes on behalf of the 40 percent holding owned by Mail.ru , the London-listed internet group backed by Uzbek-born tycoon Alisher Usmanov, Russia's richest man.
No comment was immediately available from representatives for VK, United Capital Partners or Usmanov.
At issue, say internet watchers, is control over user-generated content frowned on by the authorities. Friday's ban, despite being quickly lifted, could be a shot across VKontakte's bows to ensure it tightens its monitoring.
The network has also been accused by Russia's ombudsman for children's rights of hosting child pornography. At least one of the Boston Marathon bombing suspects had a page on VKontakte.
After Putin rose to power in 2000, the Kremlin reined in Russia's print and broadcast media, encouraging trusted business "oligarchs" to buy strategic stakes. A similar scenario, in which loyal investors ensure internet content is screened, may now be unfolding, say some commentators.
"All big media have been brought under the control of the Kremlin, and VK is the last medium that is free," journalist Nickolay Kononov, author of biography "The Durov Code", said in a recent interview.