The United States is "deeply troubled" by Russia's decision to blacklist Open Russia and two other pro-democracy groups, the State Department said late on April 28.
The Russian Prosecutor General's Office earlier this week designated Open Russia, the Open Russia Civic Movement, and the Institute of Modern Russia as "undesirable."
"We reject the notion that these and other international civil society organizations are a threat to Russia," department spokesman Mark Toner said.
"If Russia hopes to build a strong, democratic government with a dynamic, competitive economy, it should value and support, not harass and criminalize such independent voices," he said.
Russian authorities on April 27 raided the Moscow office of Open Russia, which is run from abroad by Mikhail Khodorkovsky, a former business mogul and ardent opponent of President Vladimir Putin.
The raid occurred ahead of planned protests this weekend across the country.
Toner called on the Russian government to protect human rights and stop restricting fundamental freedoms.
Former oil tycoon Khodorkovsky was Russia's richest man until Putin imprisoned him for a decade on tax evasion charges that his supporters said were politically motivated. Putin pardoned Khodorkovsky in 2013.