Prime Minister Vladimir Putin said U.S. law enforcement was out of control.
"We expect that the incident involving the arrest in the United States of a group of people suspected of spying for Russia will not negatively affect Russian-U.S. relations," a Foreign Ministry official said on condition of anonymity.
Both U.S. President Barack Obama and Russian President Dmitry Medvedev have said the "reset" of ties between the two countries after a deterioration under George W. Bush is a significant foreign policy achievement.
The Russian Foreign Ministry criticized the timing of the announcement on Tuesday, days after Medvedev met Obama in Washington, and said it did not understand why the U.S. justice department had made the news public.
The White House said Obama knew about the investigation before he met Medvedev in Washington late last week, but did not mention it during their talks.
The accusations against 11 suspects, some of whom lived quiet lives in suburbia for years, have caused a media storm in the United States.
The suspects have been accused of gathering information ranging from data on high-penetration nuclear warhead research to background on applicants for jobs with the Central Intelligence Agency.