Officers broke down the door while staffers were recording a video message.
During the raid, police allegedly seized computers and cameras from the office, tweeted the director of Navalny's Anti-Corruption Foundation, Roman Rubanov.
About 200 protesters gathered in Vladivostok, on Russia's Pacific coast, alleging that the election would be skewed in Putin's favour.
Several thousand Russians braved sub-zero temperatures to protest against President Vladimir Putin, who's seeking to prolong his nearly two-decade-long rule in March elections.
After authorities refused to register his candidacy in the election, Navalny has called on supporters to boycott the vote.
The Kremlin denies accusations of corruption and says the election will be fair, Reuters reports. Winning a new term in March would extend his presidency until at least 2024. A showed Navalny struggling with police before they pushed him to the ground and then into a bus.
Around 1,000 protesters had assembled in a square along Tverskaya Street in central Moscow despite a heavy police presence, chanting anti-Putin slogans in the sub-zero temperatures. He showed up in Pushkin Square Sunday as part of a larger cause, he says.
"You are not going there for me, it's for you and your future".
Protesters turned out in force throughout the country to have their say.
Before Navalny's public detainment, Russian police also raided his campaign headquarters, reportedly responding to a "bomb threat". "These are real citizens", Navalny wrote on Facebook.
He was held at a police precinct in central Moscow for several hours before being released without charges, his lawyer Olga Mikhailova told Reuters, adding that Navalny would face court at a later date. Police reported protests in more than two dozen cities, according to official media.
Earlier Sunday opposition supporters rallied in far eastern Russia and Siberia, including in the northern city of Yakutsk where Russians rallied despite temperatures of around minus 45 Celsius (minus 49 Fahrenheit).
"These people were just reading the news on their live stream, they weren't even calling for people" to join the protests, Navalny said in a video interview on YouTube after police made the arrests.
Navalny was arrested as he was heading to the protest.
"Putin has been in power for 18 years now", he said.
The anti-corruption activist launched the campaign after Russian officials rejected his bid to run for president last month because of a past fraud conviction that he deems politically motivated.
The Washington Post reports that thousands swarmed the streets of Russian Federation but there were not as many people as demonstrations that occurred last June.
Navalny himself served three jail sentences of 15 days, 25 days and 20 days for organising unauthorised protests previous year.