Russian President Vladimir Putin at the Kremlin in Moscow on Nov. 7. (Alexei Nikolsky/AP)

AS A magazine in print until last year, and still online today, the New Times holds a special place in the very narrow world of Russian news media that do real journalism and not propaganda. The New Times looks critically at the Kremlin and its web of power. It has explored such uncomfortable topics as the children of President Vladimir Putin’s elite, who prefer to remain in the West despite the nationalist rhetoric of their parents. The magazine also reports on corruption, and, in 2016, it published a daring cover drawing for a budget article showing Mr. Putin wearing a joker’s hat, throwing up his hands with a headline “There’s no money.” The magazine is a rare oasis in a sea of state-controlled pablum.

Now it is threatened. A Moscow court has imposed an unprecedented fine of 22.25 million rubles, or about $332,000, for failing to file a report. This is a pretext for an attack on independent journalism. The chief editor, Yevgenia Albats, a champion of investigative reporting who has long been a prominent reporter and author in Russia, and a nettlesome critic of the authorities, said the fine amounts to the magazine’s annual budget. If enforced, the fine could force it to cease operations.

The pressure began in the spring when the Russian prosecutor’s office opened a probe into the magazine’s receipt of money from the Fund in Support of Freedom of the Press. The fund was created by the magazine to receive donations from readers and other supporters. The fund had been designated a “foreign agent” under a restrictive 2012 Russian law that was part of Mr. Putin’s attempt to curtail independent voices, including nongovernmental organizations. More recently, the designation has been broadened to include news media. Ms. Albats said she believed all the money in the fund came from Russian nationals, so a report was not necessary. But the prosecutor said because it came from a fund designated a “foreign agent,” the money was foreign. The magazine immediately complied and filed a report, but the prosecutor went to court anyway, eventually winning approval of the big fine on Oct. 25.

Could it be just a coincidence that this penalty came four days after Ms. Albats interviewed the leading Russian opposition figure, Alexei Navalny, on her weekly Echo of Moscow radio show? No doubt that was the last straw. Under Mr. Putin’s soft authoritarian system, pressure is often applied indirectly at first. To suppress dissenting voices, news media owners are forced to sell out to friendly oligarchs, who install obedient journalists. Or news organizations find the tax inspectors knocking at their door. Or they find it impossible to distribute without help from the authorities, and so on. The assault on the New Times is not about filing a bureaucratic form but about whether Russia should have independent journalists who ask tough questions and publish revelatory articles. The Kremlin wants to do away with that inconvenience.