MOSCOW — After trying to silence Aleksei A. Navalny by jailing him, accusing him of money laundering and searching the homes and offices of his supporters nationwide, the Russian authorities on Wednesday took yet one more swipe at the country’s best known opposition leader.

Mr. Navalny’s organization, the Anti-Corruption Foundation, has been classified as a “foreign agent,” the Justice Ministry declared in a brief statement, a label frequently used under President Vladimir V. Putin to stigmatize groups critical of the Kremlin.

This status, first introduced in 2012 as a means to limit the activities of nongovernmental organizations by deterring foreign funding, opens the way for intrusive audits and inspections by the authorities.

The ministry said that Mr. Navalny’s group had been added to the list of “foreign agents” because it received funds totaling around $2,100 from a Florida company that sells doors, and a Spanish man.

Mr. Navalny, denouncing the ministry’s claim as lies, said in a tweet that the Anti-Corruption Foundation “never received a kopek of foreign money.” All its funding, he added, comes from Russian citizens.

“The actions of the Ministry of Justice are absolutely illegal and were taken, obviously, on direct orders from Putin,” Mr. Navalny said.

Mr. Putin, cocooned from criticism and praised nonstop on state-controlled television, has refused to utter Mr. Navalny’s name in public or even recognize his existence. But muzzling the 43-year-old opposition activist and his followers seems to have become a preoccupation for much of Russia’s law-enforcement system.

The Federal Security Service, the National Guard and other agencies last month carried out simultaneous raids on 200 sites linked to Mr. Navalny in more than 40 towns and cities across Russia. The Investigative Committee, Russia’s version of the F.B.I., announced a few weeks before that it had opened a criminal case against Mr. Navalny on money-laundering accusations. He has been sent to jail repeatedly for organizing illegal protest rallies.

Mr. Navalny has also had to contend with unidentified assailants. He was taken to a hospital in 2017 after someone threw green chemical liquid in his face and nearly blinded him.

Unlike the sycophantic announcers on state-controlled television, Mr. Navalny has appealed to a younger generation with his irreverent humor and caustic denunciations of graft, insider deals and what he calls Russia’s rigged political and economic system.

He was the driving force behind a wave of street protests in Moscow over the summer following the disqualification of opposition candidates in City Council elections. Despite facing no challenge from prominent opposition figures, the ruling United Russia party suffered significant losses in the election.

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