By 1830 Moscow time (1530 GMT), police had detained 257 protesters nationwide, according to OVD-Info, a non-governmental group that tracks the arrests.
"Your own life is at stake", Navalny, who organised the boycott protests, said in a pre-protest video.
"In order to take down our broadcast, the police cut out the door to the Anti-Corruption Foundation (FBK) office, and then began to saw the door to the studio right in the middle of broadcast", he said in a Facebook post.
He has called on supporters to continue the demonstrations despite his arrest Sunday.
Moscow's prosecutors earlier warned organizers of an unsanctioned rally along the central street against violating the legislation on organization of rallies and demonstrations.
This morning, police broke into Mr Navalny's headquarters in the Russian capital using a saw, to interrupt a live broadcast covering a series of protests in the east of the country.
Mr Navalny said he planned to attend the Moscow protest later.
Police forced their way into Mr Navalny's office and started questioning and searching people, citing reports of a bomb, an online feed run by Mr Navalny's supporters showed.
Putin has said the presidential election will be fair, and that Navalny, lacking real popular support, is irresponsibly trying to foment social anger which could tip Russian Federation back into instability.
As the crowd swelled to a few thousand people, hundreds of police armed with batons and many wearing riot helmets lined the streets leading to the Kremlin.
Navalny organized the protests as part of an effort to encourage Russians to boycott presidential election in March. Several hundred stood there, chanting, "Putin is a thief" and "Russia without Putin".
Authorities beefed up security, dispatching police vans and passenger buses to the city centre, but police largely refrained from arresting protesters.
Authorities estimated the Moscow turnout at around 1,000 people. Police searched Navalny's campaign offices in several cities ahead of the protests. "We've already endured this for 18 years".
The softer approach suggested authorities have adapted their tactics to Navalny, avoiding the mass arrests that had made global headlines past year and instead focusing on detaining the protests' organizers.
The process in which we are called to participate is not a real election. A dramatic video posted to Twitter shows police detaining Navalny and forcing him into a police vehicle.
"It's absolutely clear that the most important thing that any person can do now is to go and protest", Navalny, 41, said on his blog ahead of Sunday's demonstration.
Mr Navalny, a lawyer who has campaigned against official corruption, was barred from running in the election by the central election commission in December over what he said was a trumped up suspended prison sentence.
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This is because the each state has its own different set-up on all levels socially, financially and geographically. Each state has populations equivalent to nations with universal coverage hence size can never be a limiting issue.