Navalny has been jailed repeatedly in recent years for organising or participating in unsanctioned protests.
His Anti-Corruption Foundation (FBK) organisation has produced reports alleging corruption by top figures including Prime Minister Dmitri Medvedev.
Navalny was detained when police forced their way into his organisation’s office, according to his spokeswoman Kira Yarmysh. There was no immediate information on charges against him.
The raid came a day after Navalny said that the military conscription of one of his allies to a remote airbase in the Arctic amounted to kidnapping and illegal imprisonment.
In an interview with German news outlet Deutsche Welle, Yarmysh said police on purpose conducted the raid around the same time Navalny was going to film an episode of his YouTube show, Navalny Live.
She added that last week’s episode had close to 1.5 million views.
“They didn’t like that success,” she told DW, adding: “If they search our offices they can seize our technical equipment, so there can be no show.”
In a separate development, Russia’s top opposition newspaper Novaya Gazeta reported on Thursday that authorities had searched the Moscow apartment of its special correspondent Yulia Polukhina.
After the raid, the mother-of-two was taken to “an unknown destination,” the award-winning newspaper said in a statement.
“So far this looks like an abduction,” Novaya Gazeta said.
It added that the searches were linked to Novaya Gazeta’s publications including those concerning “illegal armed groups” operating in war-torn eastern Ukraine, where Kyiv is battling against pro-Kremlin separatists.
Authorities have been steadily ramping up pressure on Navalny and his allies in recent years with regular searches and short jail terms for the Kremlin critic and his allies.
The FBK offices were searched several times this year.