FILE - The Russian embassy in Berlin, Germany.AP
"We have decided to withdraw consent for the operation of four of the five Russian consulates operating in Germany," the spokesman told a regular government press conference.
"This was communicated to the Russian foreign ministry today," he added.
The German foreign ministry said at the weekend that hundreds of civil servants and local employees working for German institutions in Russia had been asked to leave the country.
Moscow had put a 350 limit on the number of German personnel in Russia, said the foreign ministry spokesman.
"In order to be able to meet the Russian requirements for limiting our staff, the government has decided to close the German consulates in Kaliningrad, Yekaterinburg and Novosibirsk," the spokesman said on Wednesday.
Operations will be considerably reduced and will be discontinued by November, he said.
Germany's embassy in Moscow and its consulate in St Petersburg will not be affected.
"For the Russian presence in Germany, our decisions apply reciprocally... in order to ensure a balance of the mutual presences both in terms of personnel and structure," the spokesman said.
According to the German foreign ministry, Russia will slash the number of people that Berlin can employ in its embassies or institutions in Russia in the education and cultural sectors starting from June.
Several hundred people are affected, including officials from the embassy and consulate, but mostly employees of the Goethe cultural institute in the country, German schools and nurseries, the ministry said.