Usmanov, who is reportedly worth $2.6 billion, has denied allegations that he bought the publishing house at the behest of the authorities. "This is my personal deal, my personal investment," he told the "Kommersant" daily.
Georgian entrepreneur Badri Patarkatsishvili, who purchased the newspaper from billionaire Boris Berezovsky only in February, says there "is no political subtext" behind the sale.
But his assurances have done little to soothe the concerns of "Kommersant" journalists and others concerned about the state of Russian media.
They see the deal -- reportedly worth around $300 million -- as an attempt by the Kremlin to tighten its control over mass media ahead of parliamentary elections in 2007 and presidential election in 2008.
Business daily "Kommersant" is widely respected for its independent analysis and has often been critical of the Kremlin.
The general director of the Kommersant publishing house, Demyan Kudryavtsev, has said that Usmanov does not intend to interfere in editorial policy.
Some media watchers have doubts, though. Oleg Panfilov, the head of the Moscow-based media watchdog Center for Journalism in Extreme Situations, says: "I distrust such people [Usmanov], who a year before the parliamentary and presidential elections are buying media outlets. I don't think that it is just a simple [deal]. I also think that the Kremlin is concerned that to this point several newspapers are still not under its control."
Others have expressed concern at the role of Gazprom. Usmanov is a senior manager at Gazprom, which itself has $700 million worth of media assets.
Gazprom, however, told the Interfax news agency on August 31 that it is not interested in buying the publishing group.
Freedom In Print
With the state controlling the three main television networks in Russia, newspapers are seen by some as one of the last bastions of media freedom in Russia.
In Putin's first term in office between 2000 and 2004, the state seized control of several national television channels. In 2001, Gazprom took control of NTV, then Russia's only privately owned nationwide broadcaster.
So does this mean that these small-circulation, but often influential, newspapers are next on the Kremlin's hit list?
Yury Fedorov, an associate fellow at the U.K.-based Chatham House, says that the Kremlin's first task was to tackle mass media. Now it is turning its attention to publications that target political elites.
"It's really very important for the Kremlin today on the eve of the coming presidential and parliamentary -- especially presidential elections -- to control fully not only TV channels that are normally designed to influence the masses of population but also to control elite-orientated mass media," Fedorov says.
But despite this, speaking to RFE/RL's Russian Service, "Kommersant" Editor in Chief Vladimir Borodulin plays down the implications of the deal. He says that there is a political aspect to all newspaper ownership.
"We have been living under such circumstances in which the "Kommersant' publishing house has been in the process of being sold for more than half a year," Borodulin says. "And despite who the buyer was to be -- either Alisher Usmanov, or somebody else, there was always the presumption that this guy would come to the publishing house with some political mission. Actually there is such a presumption about any new owner."