Police said they had arrested more than 20 people for trying to hold an unsanctioned demonstration at Revolution Square on Saturday.
Protest organizers say the event did not need official sanction because it was not a rally but a meeting with a parliamentary deputy from the opposition party "A Just Russia".
A similar protest was held in Saint Petersburg by Russia’s Communist party to protest to protest the recent presidential election results.
Putin, 57, won 64 percent of the vote in March's presidential election. The victory gave Putin a six-year-long term in the Kremlin. He will swear in as president on May 7.
The opposition has raised fraud allegations and called for protests, but Putin assured Russians he “won in honest and fair combat.”
Protests were also held after parliamentary vote in December, which attracted up to 100,000 people in the largest discontent in Russia's post-Soviet history.
Putin served as president for two consecutive terms from 2000 to 2008 and worked as prime minister from 2008 to 2012.