The meeting was revealed after the activist tracked social media posts of a woman who was on the boat and posted images of the two men together.
Navalny, a vocal foe of Putin who has organized large street protests on several occasions and published a series of reports alleging corruption in Russia's ruling elite, has been barred from the presidential race due to a conviction on financial-crimes charges he contends were fabricated by the Kremlin to sideline him.
The opposition leader also noted that Rybka's video filmed weeks before the 2016 U.S. election captured a conversation about former U.S. State Department employee Victoria Nuland, and connected the Deripaska-Prikhodko conversation to speculation that the oligarch could have been a link between the Russian government and the Trump campaign.
Roskomnadzor ordered YouTube's parent Google and Facebook-owned Instagram to delete the materials or face further action, the Guardian writes.
But since many internet providers don't have the technical capability to block specific URLs, complying with the order would mean removing access to YouTube and Instagram entirely. It said that the material "has been deleted" from Instagram.
Navalny found 2016 videos of Deripaska on his yacht with Sergey Prikhodko, Russia's deputy prime minister, and said Deripaska could have been bribing Prikhodko and offering information about the 2016 US election he had received from Manafort.
A February 14 deadline that Navalny said was set by Roskomnadzor passed without incident, but reports that navalny.com was inaccessible for many in Russian Federation began flowing in on February 15.
If the content is not removed from YouTube and Instagram the services could be blocked in the country, because not all providers of the internet are able to disable separate pages.
Russia's most well-known opposition figure, Navalny has been forbidden from standing against Putin in an upcoming March election.
Navalny said: "It wasn't me who took bribes from an oligarch in the form of aeroplane flights and expensive cruises, but the singular, lightning-fast attack of the government is directed against me and my foundation, who exposed the corruption".
The next day, Mr Deripaska obtained a court order demanding the removal of 14 Instagram posts and seven YouTube clips. To limit access to services have been given until Wednesday night, February 14. He inspired the largest anti-government protests since 2012 a year ago after releasing a video showing lavish estates allegedly belonging to Prime Minister Dmitry Medvedev, who denied wrongdoing.