State-run news agency RIA Novosti said around 50,000 demonstrators turned out to protest ahead of Putin's inauguration. He secured a third non-consecutive term as president during disputed March 4 elections.
Protesters shouted "fascists" as they scuffled with police. Some officers and journalists from state-run NTV channel were injured during the clashes.
Russian Interior Minister Rashid Nurgaliyev said more than 400 demonstrators were arrested during the weekend protests. Media reports showed some demonstrators dragged off by police.
"I think these images were intended for the West alone," he was quoted by RIA Novosti as saying. "We have never acted like this, but nevertheless, someone apparently needed this provocation."
Putin's spokesman suggested police were too gentle with demonstrators.
Putin, during his inauguration, vowed to protect the basic freedoms of Russian citizens.
"We want to live in a democratic country … in a successful Russia," he said.
State Duma elections and the presidential election were overshadowed by fraud allegations. Russia's constitution was amended to expand the presidential term to six years.