"The right to peaceful free speech and assembly are basic fundamental human rights and I very much regret that the authorities found it necessary to take such heavy-handed action," he said in a statement.
Earlier, French Foreign Minister Bernard Kouchner said he was "surprised" by the violence at the protests and said Russia's government should explain its actions.
Putin is running in the election as No. 1 on United Russia's slate of candidates. Opinion polls indicate the party will win at least 60 percent of the vote -- helped by Putin's personal popularity -- with rivals trailing far behind.
The 55-year-old Russian leader has said he will step down next year and hand over power to a successor in line with a constitutional ban on a head of state serving more than two consecutive terms as president.
Putin, seen by many as bringing stability after the upheaval of the immediate post-Soviet era under predecessor Boris Yeltsin, has said he will endorse one of his lieutenants as a successor; but he has refused to say which one.
Analysts believe Putin will use the endorsement he receives in the December 2 vote as a springboard to ensure he continues to play a key role in moulding policy even after next year's presidential election.
Some observers with Kremlin links have speculated that Putin might step down early and run in the presidential vote, exploiting a legal loophole to get around the three-term ban.
Russia's upper house of parliament, the Federation Council, officially named March 2 next year as the date of the presidential vote, shifting into a decisive phase the guessing game over what will happen when Putin's term ends.
After the date has been published in the official gazette on Wednesday, would-be candidates will have 25 days to apply to run in the presidential election.
The ODIHR observation team pulled out of their mission to Russia citing obstruction by Russian authorities. A spokeswoman for the body said Putin's comment about U.S. influence on the decision was "simply not true."
