The early morning raids targeted more than 100 offices and homes in 30 cities, the opposition said, including the headquarters of Navalny's Anti-Corruption Foundation (FBK) in Moscow.
An AFP journalist saw several armed interior ministry officers in black balaclavas entering the business centre hosting his offices, where agents reportedly broke through the doors to enter the premises.
Navalny, an anti-corruption campaigner who has emerged as President Vladimir Putin's most prominent critic, denounced the raids as an attempt to intimidate the opposition after a summer of protests and significant losses suffered by Kremlin allies in local elections in September.
"This will not stop us," he said in a post on his blog shortly after the raids began. "We are doing the right thing. And those who are against us are enemies of Russia."