"Russian authorities have informed us that a diplomat at the Swedish embassy has to leave the country ... Russia has made it clear it considers this to be a response to the Swedish decision to expel a Russian diplomat," foreign ministry spokesman Johan Tegel told AFP.
Neither the names nor the positions of the two diplomats were disclosed.
The Russian diplomat was expelled because of actions "not in line with the Vienna Convention" which governs diplomatic relations, Tegel said, providing no further details on the nature of the Russian's actions nor the exact timing of that expulsion.
Tegel said it was too early to tell how Moscow's decision would affect relations between the two countries.
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"But it won't improve the state of our relations," he said.
Swedish Defence Minister Peter Hultqvist said in June that Sweden, a non-NATO country, was stepping up its military capabilities and exercises with the alliance amid concerns over Russia's military resurgence.
Tensions have been rising in Sweden and the rest of the Baltic region amid signs of more assertive Russian behaviour, including Russian planes regularly skirting or violating the national air space of neighbouring countries.
The military subsequently confirmed that "a mini submarine" had violated its territorial waters, but was never able to establish the vessel's nationality.