Proekt has previously published reports exposing alleged corruption and abuses by wealthy officials close to Russian President Vladimir Putin.
Russian authorities have outlawed an investigative online media outlet and listed its journalists as "foreign agents".
The US-based publisher of Proekt was declared an "undesirable" organisation on Thursday by Russia's Prosecutor General's office.
The move to effectively ban the outlet's activities is seen as the latest in a series of steps to raise pressure on independent media in the country.
Proekt has published a number of reports exposing alleged corruption and abuses by wealthy officials close to Russian President Vladimir Putin.
But Moscow said on Thursday that its publisher -- American company Project Media Inc. -- posed "a threat to the foundation of the constitutional order and security of the Russian Federation".
Russian authorities also labelled Proekt's chief editor Roman Badanin and four of his journalists as "foreign agents".
The government already has outlawed more than thirty groups under a 2015 law that made membership in "undesirable" organisations a criminal offense. Members of an "undesirable" group face fines and up to six years in prison.
Another law will also class NGO members as "foreign agents" if they receive funding from abroad and engage in vaguely political activities.
"It's hard to imagine a better recognition," Badanin said on Facebook on Thursday, adding that he had no intention of closing his website and promising "something that will make a noise" next week.
Last month, police searched the apartments of Badanin and several other journalists, just as the outlet was preparing to release an investigation into Interior Minister Vladimir Kolokoltsev and his alleged wealth. Proekt subsequently published their report immediately after the raids.
Moscow said the searches were conducted under a defamation case over a 2017 documentary about a St. Petersburg businessman with alleged ties to organised crime.
Russian authorities have recently raised the heat on the opposition and independent media ahead of September's parliamentary election, widely seen as an important part of Putin's efforts to cement his rule ahead of the 2024 presidential election.
The influential Latvian-based Meduza website was declared a "foreign agent" in April, while VTimes closed down in June for fear of prosecution under Russian law.
The Kremlin has rejected the allegations of muzzling, saying the Justice Ministry is simply enforcing the law.