Navalny, who is mounting a long-shot bid to unseat Putin in a presidential election next year, had called for mass protests in Moscow and other cities against what he says is a corrupt system of rule overseen by Russian President Vladimir Putin.
"Alexei was detained in the entrance hall of our building," his wife, Yulia, wrote on social media. "He asked me to tell you that the plans (for the protest) are unchanged."
Reuters witnesses saw a police car leaving Navalny's apartment compound at high speed, followed a few minutes later by a minibus carrying around 10 policemen.
Electricity in his office was cut at around the same time as he was detained, briefly bringing down a live feed of nationwide protests, Navalny's spokeswoman said.
Around the venue for the planned protest, on Tverskaya Street in central Moscow, hundreds of riot police and military conscripts were waiting. Authorities have said the protest is illegal.
Reuters witnesses saw police detain a small number of protesters as they exited a metro station near the venue.
The scale of the protests will show if Navalny can build on the success of a similar event in March, in which thousands took to the streets across Russia.
Those protests were the largest since a wave of anti-Kremlin demonstrations in 2012 and resulted in over 1,000 arrests, putting rare domestic pressure on Putin, who is expected to run for and win re-election next year.
Authorities in Moscow had authorised a venue for the protest away from the city centre.
But Navalny said late on Sunday that the authorities had pressured firms into refusing to supply him and his allies with sound and video equipment, a move he said was designed to humiliate protesters.
For that reason, he said he was unilaterally switching the venue to Tverskaya Street, Moscow's main avenue near the Kremlin. The General Prosecutor's Office warned that a protest there would be illegal and police would be forced to take "all necessary measures" to prevent disorder.
A legal "caution" was being readied for Navalny, it said. Kremlin spokesman Dmitry Peskov told TV Rain, before Navalny was detained, that it was vital to avoid what he called "provocations."
The area of Tsverskaya Street near where Navalny's supporters were planning to hold their protest was hosting an officially-organised historical festival, with actors re-enacting periods of Russian history with props such as World War Two jeeps and artillery guns.
Officials had set up barriers along Tverskaya Street, and were admitting members of the public only once they had passed through airport-style metal detectors. There were long queues of people waiting to gain access.
Reuters reporters saw a heavy police presence on and around the avenue with bus loads of riot police parked nearby and side roads blocked off.
Navalny election hopes
For now, polls suggest Navalny has scant chance of unseating Putin, who enjoys high ratings. It is unclear too if the Kremlin will even let Navalny run for the presidency.
But the 41-year-old lawyer turned political street campaigner hopes anger over corruption may boost his support.
A video he made accusing Prime Minister Dmitry Medvedev, a Putin ally, of living far beyond his means has garnered over 22 million online views to date.
Medvedev said Navalny's allegations were politically motivated "nonsense" and called him a charlatan.
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.
The Moscow protest is due to run from 1100 to 1400 GMT.
"I want changes," wrote Navalny in a blog post last week. "I want to live in a modern democratic state and I want our taxes to be converted into roads, schools and hospitals, not into yachts, palaces and vineyards."
(Additional reporting by Christian Lowe, Jack Stubbs, Maria Tsvetkova, Sveta Reiter, Dmitry Solovyov, Gleb Stolyarov, Anton Zverev in Moscow and Natasha Shurmina in Ekaterinburg; Writing by Andrew Osborn; Editing by David Evans and Richard Balmforth)
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)