Russia expelled two German diplomats in what it called a standard diplomatic response to a similar move by Germany last week.
Russia also said it hoped a dispute over the killing of a Georgian citizen in Berlin would not damage ties further.
Germany's foreign ministry announced the expulsion of two Russian diplomats last week over what it said was Russia's refusal to cooperate in the investigation of a murder in which German prosecutors suspect Russian or Chechen involvement.
The Russian government has denied connection with the killing.
Russia's Foreign Ministry today summoned the German ambassador in Russia to issue a formal protest over the expulsions and gave two German diplomats seven days to leave the country, it said in a statement.
"These measures were unavoidable after two of our diplomats were expelled. We consider the move by Berlin to be absolutely unfounded," Russian spokesman Dmitry Peskov said.
"We expect and hope that this will not become a negative factor for the further development and broadening of our constructive dialogue," he told reporters on a conference call.
Tensions between Russia and Western countries including Germany have resurged since the poisoning last year of a former Russian spy, Sergei Skripal, and his daughter on British soil.
Germany traditionally has close business ties with Russia and the diplomatic row came as Russia is building a major natural gas pipeline to Germany, Nord Stream 2, despite US opposition.
Germany's Foreign Ministry said it regretted the move by Russia to expel the German diplomats."It sends the wrong signal and is unjustified," it said.
Georgian citizen Zelimkhan Khangoshvili was shot dead in Berlin in August as he was heading to a mosque.
Russian President Vladimir Putin said this week Mr Khangoshvili himself was a killer who had carried out bloody acts on Russians oil and that the Russian government's requests for his extradition had not been heeded.
Germany contradicted that yesterday, saying it was not aware of any extradition requests made by Russia.
Today, Russia insisted it had sought Mr Khangoshvili's extradition.
"There were requests. The man took part in acts of terrorism and mass murder," Mr Peskov said.