The regional arbitration court ruled in favour of a state firm which sued the consulate over some 74 million rubles (USD 1.1 million, 960,000 euros) in unpaid rent, demanding that its staff be kicked out of the Saint Petersburg location.
Consulate officials "must pay Inpredservice debts in the amount of 74 million rubles and move out of the building," the court's press service said. Polish diplomats have occupied two city centre buildings since 1983.
A representative of Inpredservice, Alexei Chernykh, was cited by Russian news agencies as saying there was "no political context" to the ruling, and that Poland is simply the only consulate in the city which is not paying its bills.
In a comment to Interfax news agency, the Polish embassy in Moscow said the decision to evict goes against the Vienna Convention on diplomatic relations.
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Embassy officials added the consulate stopped paying because Russia hiked the rates tenfold while using space for its diplomatic offices in Poland for free.
Fresh tension was injected into ties when Poland's Foreign Minister Grzegorz Schetyna angered Moscow by crediting Ukrainian soldiers, not the Red Army, with liberating Auschwitz ahead of 70th anniversary ceremonies last week.
Polish President Bronislaw Komorowski then appeared to make amends by paying tribute to Soviet troops as liberators.
He has since created another stir by floating the idea of Poland hosting May 8 ceremonies marking the 70th anniversary of the end of World War II.
Observers believe that given the heightened East-West tension over the Ukraine crisis, Komorowski could be planning the event as a way of giving Western leaders an "out" from attending high profile military celebrations scheduled on May 9 in Moscow.