Sergei Udaltsov, leader of the radical opposition Left Front, said hundreds of people were taken into custody after refusing to leave Pushkin Square at the end of a sanctioned rally, RIA Novosti reported.
Well-known opposition figurehead Alexei Navalny was among those detained, the Russian news agency said.
The rally came the day after a landslide election victory for Putin, who was forced by term limit laws to step down as president in 2008 after serving two consecutive terms.
Protest organizers alleged widespread violations in this year's election. Police say there were 14,000 people at the rally that began in Pushkin Square, while organizers say it was closer to 20,000.
Police say they stopped protesters from heading toward the Kremlin.
Abljt 100 people were also arrested at a separate rally near the office of the Central Elections Commission, RIA Novosti said.
With 99.5 percent of ballots counted, Russia's presidential elections Sunday saw Putin claim a landslide victory, capturing 63.71 percent, RIA Novosti said. Communist leader Gennady Zyuganov received 17.19 percent, while billionaire-turned-politician Mikhail Prokhorov got 7.88 percent.
Putin said Monday he plans to tell the Central Election Commission to investigate possible voting violations, RIA Novosti said.
During a meeting with several election rivals, Putin said he would "have a conversation" with elections chief Vladimir Churov and "will ask him to thoroughly look into all possible violations ... ."
An international monitoring agency reported Monday it found state resources were used at the regional level to support Putin's candidacy. Also, overly restrictive candidate registration requirements limited genuine competition.
The Organization for Security and Cooperation in Europe, based in Austria, said in a statement voting generally was positive. However, monitors said nearly a third of polling stations had procedural irregularities.
"This election showed a clear winner with an absolute majority, avoiding a second round. However, [a] voter's choice was limited, electoral competition lacked fairness and an impartial referee was missing," said Tony Kox, head of the delegation to the Council of Europe's Parliamentary Assembly.
Presidential candidates could not "compete on an equal footing" and despite efforts to improve transparency, "there remained widespread mistrust in the integrity of the election process," said Ambassador Heidi Tagliavini, leader of the organization's election observation mission. "As a first step, all allegations of electoral violations need to be thoroughly investigated."
The independent election watchdog Golos, a U.S.-funded non-governmental organization, said Putin won more than 50 percent of the vote.
It reported fraud allegations, including "carousel voting," in which the same people cast ballots at multiple locations, and "centralized voting," in which managers of factories, schools, hospitals and other large organizations pressure employees to vote for a specific candidate. In some cases, ballots are collected at the workplace.