"Twenty-nine people were detained by police for breaches of public order," the city police's press service said.
Opposition supporters had begun to walk peacefully along the city's main Tverskaya Street from a central metro station at around 1030 GMT in an event coordinated via social media.
Police in helmets and body armour swiftly moved to halt a protest which drew around 100 people.
An AFP photographer at the scene said people were detained as they simply walked along the street, without shouting slogans. One man holding a poster was detained first.
The latest detentions came after Navalny organised protests in cities across Russia on March 26, most of them unauthorised.
The largest rally in Moscow saw about 500 people detained according to police, while OVD-Info, a website that monitors detentions of activists, put the total at almost 1,000.
Navalny called the protest over his anti-corruption investigation into Prime Minister Dmitry Medvedev linking the latter to huge mansions and vineyards in a video report garnering more than 16 million views on YouTube.
Among those protesting on Sunday was a 16-year-old boy called Pavel Dyatlov who became a symbol of youth protest in last week's rally after being photographed climbing up a lamppost and being detained by police.
Dyatlov told AFP he had come back to protest on Sunday after reading about it on social media, saying the protest was "calling for the current government to stand down, or for early presidential elections."
"We were heading towards Red Square and the police started to push us back," he said before police detained him again.
Witnesses said police targeted people photographed at the previous rally.
"Right from the start I saw that they were detaining children and 'faces from the the media' -- you could see they were acting in a targeted way," said 70-year-old Natalya Ponomarenko from the Moscow region, who also attended last week's rally.
"I came here a second time to see what the result of March 26 would be," she said, stressing that the participants were peaceful and "the plan was to go for a walk."
OVD-Info reported at least 32 people were detained Sunday, including at least four minors.
Navalny 'knows nothing about this'
Posts on Facebook linked the latest protest to little-known nationalist group Novaya Oppozitsiya, or New Opposition, which called for people to turn out in support of those detained last week.
Navalny, who is currently serving a 15-day sentence behind bars for disobeying police at last Sunday's demonstration, distanced himself from Sunday's event.
"He knows absolutely nothing about this," his spokeswoman Kira Yarmysh wrote on Twitter.
The authorities earlier Sunday laid on a massive police presence in anticipation of an unauthorised protest on Red Square.
Journalists saw only a handful of activists there, however, some of whom voiced support for President Vladimir Putin. OVD-Info reported 11 arrests.
In the large Siberian city of Novosibirsk, around 400 people turned out for an authorised anti-corruption rally, Interfax news agency reported.
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