The move represents a sharp downgrading of bilateral ties amid a wider collapse in relations since Russia's invasion of Ukraine early last year.
Russia denounced the proposed closures as ill-conceived and provocative and said it would respond.
Germany's foreign ministry accused Moscow of escalating tensions by imposing limits on numbers of German officials. "This unjustified decision is forcing the federal government to make very significant cuts in all areas of its presence in Russia," a spokesperson said.
The Russian government would be still be allowed to operate its embassy in Berlin and one general consulate, but Germany expects the rest to cease operations by the end of the year, the ministry said.
Germany will close its own consulates in Kaliningrad, Yekaterinburg and Novosibirsk, leaving only the German embassy in Moscow and the consulate in St Petersburg in operation.
In Moscow, the Russian foreign ministry condemned what it called "yet another unfriendly step aimed at the further destruction" of bilateral ties. Berlin's actions "will not go unanswered by us," it said in a statement without giving details.
Relations between Russia and Germany, which used to be the biggest buyer of Russian oil and gas, have broken down since the invasion in February 2022 and the West responded with sanctions and weapons supplies.
Germany is planning to remove scores of employees working at its missions in Russia after Moscow imposed limits on the numbers allowed to work in the country.
(Additional reporting by Caleb Davis and David Ljunggren, Writing by Friederike Heine and Matthias Williams; Editing by Madeline Chambers, Alison Williams and John Stonestreet)
By Andreas Rinke and Alexander Ratz
