The Foundation for Fighting Corruption, which focuses on major investigative reports in Russia, has been added to the foreign agents registry, the Russian Justice Ministry announced Wednesday without giving a reason for listing.
Russian officials have previously used the law to stigmatize various nonprofits, including highly respected human rights organizations.
Navalny and his foundation, known by its Russian acronym FBK, have been careful over the years not to use foreign funding in order to avoid being on the foreign agents list, as well as avoiding accusations of foreign interference.
The Russian government has routinely dismissed the opposition as rioters on the payroll of Western governments.
Navalny, who has been jailed repeatedly for organizing protests, has issued numerous reports on Russian corruption. He is perhaps the most well-known political challenger to President Vladimir Putin and his foundation was a major force behind anti-government rallies in Moscow this summer.
In a series of tweets Wednesday, the 43-year-old opposition leader rejected the allegations that the group accepted foreign funding and urged Russian authorities to release evidence to back up their claim.
"All of FBK's money comes from your donations - that of Russian citizens," he said. "The justice ministry's actions are totally unlawful and are clearly done on (President Vladimir) Putin's order."
FBK, which reports its sources of funding every year, rose to prominence thanks to its crowdfunding of numerous investigations into corrupt Russian officials and their ill-gotten wealth.
In recent years, the foundation has grown into a nationwide network of Navalny's supporters who have been investigating local officials and staging opposition rallies in their regions.
Wednesday's listing comes on top of a series of arrests and criminal charges against opposition leaders and activists.
In the most recent tactic against the opposition, several government-owned bodies and enterprises including the Moscow subway have been suing opposition figures for damages over this summer's protest rallies. The total damages the opposition will have to pay, unless the rulings are overturned on appeal, already exceed $280,000.
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