He is also accused of creating a non-commercial organisation and encouraging Russians not to perform "their civic duties" by publishing an investigation into Putin's alleged wealth, Navalny said.
Navalny in January released a probe into a Black Sea palace Russian tycoons allegedly built for Putin which has racked up more than 116 million views on YouTube. Putin denies that the palace is under his possession.
Navalny was arrested in January upon returning from Germany after recovering from a nerve agent poisoning attack he says was orchestrated by the Kremlin. The Kremlin denies the allegation.
He is serving two-and-a-half years in a penal colony outside Moscow on old fraud charges he says are politically motivated. He is a target of several other probes.
Navalny announced the new charges against him as pressure builds on the opposition ahead of parliamentary elections in September.
Next month a court will hear whether to add Navalny's network of regional offices and his Anti-Corruption Foundation to a list of "terrorist and extremist" organisations.
In another move targeting his supporters, Russia's lower house of parliament this month approved legislation in a first reading that would ban members of "extremist" organisations from becoming lawmakers.
The second reading of the bill was set to take place on Tuesday.