Human Rights Watch published a 78-page report Wednesday highlighting the "crackdown on civil society" that followed Putin's election to a third non-consecutive term in May.
Government critics were denied a permit to protest last month. Putin's re-election last year was marked by widespread protests and his government has since jailed several opponents.
The rights community expressed recent concern over laws passed in Russia that expand the definition of treason. A crackdown on the role of non-governmental organizations, passed in July, was equally problematic for Human Rights Watch.
Director of European and Central Asia programs at Human Rights Watch Hugh Williamson said Putin's administration has harassed opponents and the rights community. It's labeled critics as "clandestine enemies."
"The government crackdown is hurting Russian society and harming Russia's international standing," Williamson said in a statement.
The Moscow offices of Human Rights Watch, Amnesty International and Transparency International were raided by Russian authorities last month.
Russian authorities described the raids as routine. A government spokesman didn't reply to questions Wednesday from state-owned news agency RIA Novosti, which reported the offices of independent pollster Levada Center were raided on allegations of using foreign funds.
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