Dmitri S. Peskov, a spokesman for Mr. Putin, said that as far as he knew, Mr. Guriev had simply left Russia on vacation, and that he could not comment on the investigation. “This is not our question. This has nothing to do with the Kremlin, nothing to do with the president,” he said. “The only thing I can tell you is that this is pure speculation.”

Commenting on Mr. Guriev’s case on Wednesday, the pro-Kremlin analyst Sergei A. Markov wrote that institutions like Skolkovo and the New Economic School had been used to funnel funds to demonstrators.

“The sudden departure of Guriev is connected to the attempt to keep out of the hands of investigators these secret channels, through which oligarchic and federal budgetary funds went to support the revolutionary anti-Putin opposition,” Mr. Markov said. “The goal was, of course, not direct revolution, but for Putin to give up his intentions to return for a third term.”

A year after Mr. Putin’s return, the balance between liberals and hard-liners in his government has changed rapidly, and a shadow of suspicion has fallen over much of Mr. Medvedev’s legacy. Mr. Medvedev’s team is now seen in the Kremlin as sympathetic toward the opposition, and it draws even more suspicion than the protesters themselves, Mr. Makarkin said.

Mr. Guriev was a rare figure who straddled the worlds of Moscow elites and opposition activists, which seemed to overlap momentarily when anti-Putin protests broke out in late 2011.

Though his wife, herself a prominent economist, moved to France several years ago, Mr. Guriev remained in Russia. He threw his energy into persuading talented, Western-educated Russian academics to return to Russia to teach, said Erik Berglof, chairman of the New Economic School’s international advisory board. “He certainly was someone who believed that Russia could change,” Mr. Berglof said, adding that the board has begun searching for his successor. “He will be greatly missed, but the school existed before Sergei joined and will continue to develop after he has left.”

Mr. Guriev has not offered any details of his interactions with investigators, but one of the other collaborators on the Khodorkovsky report — a team convened by Mr. Medvedev’s human rights council — said investigators nearly picked apart his organization in search of evidence that it had received money from Mr. Khodorkovsky.