In a challenge to President Vladimir Putin on his 65th birthday, protesters rallied across Russia on Saturday, heeding opposition leader Alexei Navalny's call to pressure authorities into letting him enter the presidential race.

Police allowed demonstrators in Moscow to rally near the Kremlin in an apparent desire to avoid marring Putin's birthday with a crackdown. A bigger rally in St. Petersburg, Putin's hometown, was disbanded by police after protesters blocked traffic and attempted to break through police cordons.

The rallies came as Navalny himself is serving a 20-day jail term for calling for an earlier unsanctioned protest.

In Moscow, several hundred protesters, most of them students, gathered on downtown Pushkinskaya Square, waving Russian flags and chanting "Russia will be free!" and "Let Navalny run".

Riot police officers detain a protester during a rally in St Petersburg on Vladimir Putin's birthday. (AP)

Police warned them that the rally wasn't sanctioned and urged them to disperse, but let the protest continue for hours without trying to break it up.

Mostly teenage protesters later walked down Moscow's Tverskaya Street toward the Kremlin, shouting "Putin, go away" and "Future without Putin".

Police lines blocked them from approaching Red Square and they turned back. Several hours later, some made a new attempt to march on the Kremlin, shouting "Putin thief" and briefly attempted to block traffic.

"We battle for Russia to be free from Putinism. Because the power we have now is feudal, we have no freedom of speech, no freedom of choice," said protester Stepan Fesov.

A blood-soaked protester is detained in St Petersburg on Vladamir Putin's 65th birthday. (AP)

The authorities' decision to refrain from breaking up the Moscow protest contrasted with a more forceful response to previous Moscow rallies called by Navalny, when police detained more than 1,000 demonstrators.

Police also didn't intervene at first with a bigger unsanctioned rally in St Petersburg, where nearly 2,000 gathered at Marsovo Pole park and then marched across the city chanting "Russia without Putin" and "Putin, retire".

Shortly after, police broke up the demonstration, detaining nearly 40 after some tried to break through police lines. Police said those detained were released and will face fines for blocking traffic.

A protest in Putin's hometown was disbanded after demonstrators blocked traffic and attempted to break through police cordons. (AP)

One detainee, Marina Bukina, said she was injured in the head when a police officer hit her with a club.

After the St Petersburg march was disbanded, several hundred protesters continued rallying for hours at the downtown Vosstaniya Square as police stood by without intervening.

"Putin has been in charge since I was born," said Dmitry Samokhin, an 18-year-old protester in St Petersburg. "The country is mired in stagnation and I want to see changes."

Navalny's headquarters called protests in 80 cities. Most were not sanctioned by authorities, but police largely refrained from dispersing the rallies that drew from a few dozen to a few hundred people. The Siberian city of Yakutsk saw a tough police response, with a few dozen demonstrators reportedly detained.

Riot police officers block protesters with Russian flags during a rally in Moscow on Vladimir Putin's birthday. (AP)

Navalny has declared his intention to run for president in the March 2018 election, even though a criminal conviction that he calls politically motivated bars him from running. The 41-year-old anti-corruption crusader has organized waves of protests this year, raising the pressure on the Kremlin.

Putin hasn't yet announced whether he would seek re-election, but he's widely expected to run. With his current approval ratings topping 80 percent, he is set to easily win another six-year term in a race against torpid veterans of past election campaigns, like Communist Party chief Gennady Zyuganov.

Navalny argues that the high level of support for Putin comes from the lack of real political competition and urged supporters to help him get registered.

"(Putin's) 86 percent approval rating exists in a political vacuum," he said. "It's like asking a person who has been fed rutabaga his entire life how eatable they find it and the rating will be quite high. Listen, there are other things that are better than rutabaga."

Russian opposition leader Alexei Navalny. (AP)

The sarcastic analogy demonstrated Navalny's stinging style, which has helped him win broad support among the young.

Navalny has worked to expand his reach with videos exposing official corruption and YouTube live broadcasts. His documentary about Prime Minister Dmitry Medvedev's alleged ill-gotten wealth has been viewed nearly 25 million times since its release in March, helping galvanize protests.

Following Navalny's call, tens of thousands took to the streets in dozens of cities and towns across Russia in March and June in the biggest show of defiance since the 2011-2012 anti-government protests.

Unlike those past rallies, which were driven by anti-corruption slogans, Navalny this time focused on rallying support for his own presidential bid — a reason some gave for the smaller protest in Moscow.