It looked like a scene from a primetime drama. At 11.20am, masked police cradling Uzi-style machine guns burst into the HQ of Russia's National Reserve Bank. Sitting upstairs was Alexander Lebedev, the corporation's sneaker-wearing boss and billionaire proprietor of the Independent and London Evening Standard newspapers.

As officers raced up the stairs, it was unclear if Lebedev was about to be carted off to jail – a risk for Russia's nervous rich. "He may be arrested," Lebedev's aide Artyom Artyomov said, describing how 20-30 masked men in black uniforms had stormed into the 11-storey building in Moscow. From outside it was impossible to see through its green-tinted windows.

Rapidly it became clear that Lebedev was not under arrest – at least not yet. Artyomov said police thoroughly searched the bank's headquarters and its second branch in Moscow. "They are confiscating documents in both places," he said.

Lebedev was talking to police, but was unhappy about the ostentatious nature of the search, redolent of Russia's lawless 1990s, the aide added. "What really upsets us is this 'masky' show. We thought things like this were a thing of the past," Artyomov said. "He doesn't understand why there is a need to create such a circus."

Officially, the raid appeared to be connected to a short-term loan from Russia's central bank to Lebedev's corporation.

Unofficially, however, those familiar with the opaque dealings of the Kremlin were scrambling to work out the subtext. As well as his British titles, Lebedev owns Novaya Gazeta, Russia's crusading liberal newspaper, a perpetual thorn in the Kremlin's side. But Lebedev is cautious to avoid direct criticism of Vladimir Putin or Dmitry Medvedev. He describes himself, perhaps fancifully, as a loyal oppositionist.

The raid – masterminded by the economic division of Russia's FSB spy agency – may have been carried out to upstage the trial of Mikhail Khodorkovsky, the Kremlin critic jailed since 2003. The oligarch's second trial has been grinding on for 18 months and Todayhe gave his final words before a verdict.

Alternatively, the raid may have been a rebuke after Mikhail Gorbachev told the BBC last week that Medvedev and Putin were "doing everything they can to move away from democracy, to stay in power". Lebedev and Gorbachev are good friends.

It reinforces the precariousness of Lebedev's Russian business empire. Novaya Gazeta reported that investigators involved in the search were interested in documents relating to another bank, Rossiysky Kapital. Lebedev's bank was involved in bailing it out in 2008.

The paper commented: "You don't need a high legal education to guess that the documents of Rossiysky Kapital are in that bank, and not in the offices of businessman Lebedev. The people carrying out the search were informed of that, but the young investigators said the search would go ahead in any case and Lebedev himself could be 'closed'" – a euphemism for "put in prison".

Lebedev told the Guardian last year he had been tipped off that law enforcement agencies were investigating his affairs and he had been advised to take a holiday from Russia. He now faces a tricky choice – fleeing to London, as other tycoons have, or toughing things out.