Navalny, who had a green liquid thrown in his face in April, robbing him of some of his sight, said hundreds of people had attended demonstrations in Russia's Far East on Monday morning. More than 1,000 people have been arrested across Russian Federation.
Almost 200 rallies were planned for towns and cities to mark the Russia Day public holiday.
More than 1,000 protesters were arrested at a similar rally March 26.
Servicemen of the Russian National Guard gather during the anti-corruption protest in Moscow.
Navalny himself was detained as he left his home to head to the Moscow event.
Thousands took to the streets in other cities across Russian Federation, with the authorities sanctioning some gatherings and banning others.
A regional security official, Vladimir Chernikov, told Ekho Moskvy radio that police wouldn't interfere with demonstrators on the street - as long as they didn't carry placards or shout slogans.
In St. Petersburg, an Associated Press reporter counted about 500 people forced into police buses.
The demonstrators appeared to skew predominantly younger - those who were born o.
The opposition leader - who plans to run against Vladimir Putin in next year's presidential election - said earlier they would go ahead regardless of whether the government allowed them or not.
Navalny was among those arrested Monday.
Protests against corruption that were organized by opposition activist Alexei Navalny and his supporters took place in many Russian cities on June 12.
Riot police were out in full force on Monday, hungrily roaming through the crowds, looking for people holding up signs or anything that indicated they were protesting.
"Alexei has been detained in the stairwell", she wrote.
"The rally is absolutely peaceful, it isn't a protest, just a gathering of people who want to express their views", said Anastasia Lukanina, 30.
A crackdown on peaceful protests across Russian Federation in which hundreds of people were arrested and numerous others beaten by police demonstrates the authorities' utter contempt for fundamental human rights, Amnesty International said today. That means the protest will be illegal in the authorities' eyes and that riot police could be ordered to move in to break it up.
Reuters witnesses saw police detain a small number of protesters as they exited a metro station near the venue. Police said later he had been detained for violating the laws on rallies and disobeying a police officer.
By calling people to an unauthorised rally, Alexei Navalny knew he was risking a confrontation.
Back in March, thousands of people came out to anti-Putin protests across the country that Navalny helped spearhead through his social media outlets.
Mr Navalny angered officials in Moscow after he made a last-minute decision to change the main protest's location to one of the city's busiest thoroughfares. He said interference had prevented contractors from building a stage at the agreed venue.
There was also a large police presence in St. Petersburg, where protesters chanted "shame" during a rally at the Field of Mars park. Police began randomly detaining people gathered near McDonald's at the top of Tverskaya Street, where hundreds waited to follow the crowds.
Electricity in his office was cut at around the same time as he was detained, briefly bringing down a live feed of the protests, Navalny's spokeswoman said.
Navalny's Fund for Fighting Corruption had been providing updates on protests throughout the country Monday.