The rights organization says "tens of thousands of protestors" flocked to downtown Moscow on the eve of the inauguration for Putin. Putin secured a third non-consecutive term as president during a March election that was allegedly tilted in his favor.
Human Rights Watch said Russian police used rubber clubs against demonstrators. Hugh Williamson, director of Europe and Central Asian affairs at the rights organization, said while some protesters were out of line, police had reportedly acted aggressively.
"We are also concerned about allegations of police brutality, including beatings and causing unnecessary pain and suffering," he said in a statement.
State-run news agency RIA Novosti said around 50,000 demonstrators turned out to protest ahead of Putin's inauguration.
Russian Interior Minister Rashid Nurgaliyev said more than 400 demonstrators were arrested during the weekend protests. He suggested the demonstrations were staged for the benefit of the West.
Putin's spokesman suggested police were too gentle with demonstrators.
Putin, during his inauguration, vowed to protect the basic freedoms of Russian citizens.