He was detained at his home in Moscow earlier on Monday, ahead of anti-corruption demonstrations in Russia.
Hundreds of people were held during the gatherings across the country.
Riot police in central Moscow were picking protesters out of the crowd at random, a BBC correspondent at the demonstration has said.
The 41-year-old opposition leader later confirmed this in a tweet on his Twitter page (in Russian).
Mr Navalny, who intends to stand for the Russian presidency next year, had been due to attend the unauthorised rally in the capital earlier on Monday.
OVD-Info, an independent NGO, said that 825 people had been detained at the protest in the capital.
Police in Moscow say about 5,000 took part in the demonstration there, Interfax news agency reports.
Russia’s interior ministry says about 3,500 people attended the protest in the north-western city, and 500 were detained.
At first it was hard to tell who was taking part. Tverskaya Street was full of families marking Russia Day with entertainers in historical costumes.
Then thousands of protesters turned up. Huge numbers of riot police were right behind them.
By calling people to an unauthorised rally, Alexei Navalny knew he was risking a confrontation. The police duly obliged.
But people I spoke to said they knew the risk and still wanted their voices to be heard. Among other things, those voices chanted loudly: “Putin, thief!” and “Russia will be free”.
Mr Navalny was earlier granted permission to hold a rally at Sakharova Avenue but changed the location – without permission – on the eve of the demonstration to Tverskaya Street, near the Kremlin.
The protest was called over government plans to demolish Soviet-era apartment blocks in the city.