In Moscow the authorities rejected an application from Navalny's supporters to protest in the city centre, raising the possibility that the police may disperse the rally by detaining people, as they have often done in the past.
OVD-Info says 291 people were detained in 19 cities. In Moscow police beat members of a crowd of about 5,000 with truncheons in Pushkin Square, according to video published by the opposition newspaper Novaya Gazeta.
Opponents of the pension reforms, which envisage raising the retirement age for men to 65 from 60 and to 60 from 55 for women, staged protests across Russian Federation as voting took place.
Russia's ruling United Russia Party suffered a rare setback in regional elections on Sunday despite winning most of the seats, a reversal its leaders and election chiefs blamed on unpopular plans to raise the pension age.
OVD-Info, a rights organisation that monitors detentions, said 839 people had been detained by police on Sunday in 33 cities, including some of Navalny's closest aides.
The results in weekend voting for heads of about one third of Russia's regions were the worst for United Russia, which backs President Vladimir Putin, since elections for regional leaders were re-introduced in 2012.More news: Olivia Newton-John, 69, reveals the tragic cancer diagnosis she kept secret
Mr Navalny had planned to lead the Moscow protest - but last month he was sentenced to 30 days in prison for breaking laws around public demonstrations.
It said 129 were held in the Urals city of Yekaterinburg, 60 in the southwestern city of Krasnodar, and 48 in Perm in the Ural Mountains.
From 2019, the retirement age for men and women will start being increased gradually. Photos and video footage from St. Petersburg show the police violently beating protesters. However, the unexpected effect is that Putin, by closing off politics to liberal parties, has only strengthened the Communist Party as the main opposition party.
Viktor Fedoseyev and Vasil Kostylev, who were detained in central Moscow in connection with the protests, have been charged with assaulting an officer, according to the Open Russia civic movement established by former Russian tycoon and Kremlin foe Mikhail Khodorkovsky.
Raising the pension is opposed both by older people, who fear they won't live long enough to collect significant benefits, and by younger Russians anxious that keeping people in the workforce longer will limit their own employment opportunities.
Sputnik English reported on an "unauthorized march" in Moscow with about 2,000 protesters rallying against the pension reform. Last month he offered some concessions, but he and government officials said the age hike is necessary because rising life expectancy in Russian Federation could exhaust pension resources if the eligibility age remains the same.