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The Russian Federal Security Service, or F.S.B., said in a statement that Mr. Gershkovich “is suspected of spying in the interests of the American government” and had been detained in Yekaterinburg, a city about 900 miles east of Moscow in the Ural Mountains.

Hours later, the Kremlin endorsed Mr. Gershkovich’s arrest. “We’re not talking about suspicions,” Dmitri S. Peskov, spokesman for President Vladimir V. Putin of Russia, said, adding, “He was caught red-handed.” Mr. Peskov said he could not provide further details.

The detention is an ominous sign for the rights of foreign journalists based in Russia. The Wall Street Journal strongly rejected the accusations against Mr. Gershkovich and said it would seek his immediate release. “We stand in solidarity with Evan and his family,” the newspaper said in a statement.

The Biden administration said it was “deeply concerned” by Mr. Gershkovich’s detention, and State Department officials had contacted Russian authorities to secure access to the reporter and check on his welfare.

“The targeting of American citizens by the Russian government is unacceptable,” Karine Jean-Pierre, the White House press secretary, said in a statement. “We condemn the detention of Mr. Gershkovich in the strongest terms. We also condemn the Russian government’s continued targeting and repression of journalists and freedom of the press.”

Mr. Gershkovich, 31, has worked for The Journal in Moscow since January 2022 and previously reported in Russia for Agence France-Presse and for The Moscow Times. Before that, he was a news assistant for The New York Times, based in New York.

No Western journalist has been tried on espionage charges in Russia in recent years. But in March 2022, many foreign news organizations temporarily removed their reporters from the country after harsh new laws virtually outlawed some forms of independent reporting after the invasion of Ukraine.

Since then, correspondents — including Mr. Gershkovich — had continued to receive accreditation from the Russian Foreign Ministry and had generally been able to operate freely.

But American journalists, in particular, have been concerned about a situation like the one now unfolding with Mr. Gershkovich: that Russian authorities might detain a correspondent from a U.S.-based organization amid the larger tensions between the two countries.

“Until today, there was a hope among foreign correspondents working in Russia that these crackdowns on independent reporting would not extend to them,” said Gulnoza Said, a coordinator at the Committee to Protect Journalists, which monitors press freedoms abroad. “But with these very serious charges, it is clear that any foreign correspondent could be a victim.”

“The situation was frozen,” she added, “and now it got worse. Everybody working in Russia knew it may happen, but everyone was hoping it would not.” Ms. Said called for Mr. Gershkovich’s immediate release, joining media advocacy groups like the National Press Club that decried “an unjust detention.”

Mr. Gershkovich faces up to 20 years in prison under Russia’s criminal code. Espionage trials in the country can take months and are typically conducted in secret. Acquittals are virtually unheard-of.

Photos and video appeared to show Mr. Gershkovich exiting a court building in Moscow on Thursday afternoon with a jacket hood over his head. He pleaded not guilty to espionage charges, the Russian state news agency Tass reported.

In past espionage cases, after a guilty verdict, Russia has sought an exchange for a Russian spy held in the West. In 2019, in exchange for two convicted Russian spies in Lithuania, Moscow freed a Norwegian man who had been held for 23 months on accusations of espionage.

The detention of Brittney Griner, an American W.N.B.A. star, on a minor drug charge in February 2022 set off a monthslong negotiation between Moscow and Washington for her release, culminating in a prisoner swap that freed a Russian arms dealer from U.S. custody.

American officials have also pushed for the release of Paul Whelan, a former Marine who has been held in Russia since 2018 and sentenced to 16 years in prison for what the United States considers sham espionage charges. His brother, David Whelan, said in a statement that he hoped the Biden administration “moves quickly and decisively” to secure the release of Mr. Whelan and Mr. Gershkovich, although he also questioned if the White House considered his brother’s case a priority.

On Thursday, Russia’s deputy foreign minister, Sergei A. Ryabkov, signaled that it was too soon to discuss a swap for Mr. Gershkovich. “Certain exchanges that took place in the past took place for people who were already serving sentences,” Mr. Ryabkov told reporters, according to the Russian news agency Interfax, adding, “Let’s see how this story will develop.”

Tatiana Stanovaya, a senior fellow at the Carnegie Russia Eurasia Center who is based in France, said that Mr. Gershkovich’s reporting on the Russian military was what had most likely attracted the attention of the Russian security services, adding that they probably saw an opportunity to gain a new negotiating chip.

“I think that it will attract a lot of attention politically in the United States so that the authorities will have to react,” she said, adding that his arrest “puts the Kremlin in an advantageous position.”

Mr. Peskov, the spokesman for Mr. Putin, said that the Kremlin was not planning to shut down The Journal’s Moscow bureau. “Those that are carrying out normal journalistic activity, if they have a valid accreditation, then of course they will continue to work,” he said.

The Journal recently named a new top editor, Emma Tucker. In 2014, as deputy editor of The Times of London, Ms. Tucker was closely involved in an episode involving two correspondents who had been kidnapped and detained in Syria. One of the journalists, Anthony Loyd, was shot twice in the leg, and the other, the photographer Jack Hill, was beaten up before the men were able to escape.

“We are very concerned for the safety of Evan and will keep you informed of the situation,” Ms. Tucker wrote in a Thursday memo to her staff.

Victoria Kim contributed reporting.