Already tense relations between Warsaw and Moscow have hit new lows since Russia's invasion of Ukraine in 2022.
Poland says its own role as a hub for aid for Kyiv has made it a target of Russian sabotage, cyberattacks and disinformation - allegations that Moscow denies.
"The ambassador was invited to the ministry at 1500 (2300 AEST)," foreign ministry spokesman Pawel Wronski said on Monday.
On Sunday, Prime Minister Donald Tusk said Poland knew "for sure" that Russian secret services were behind the huge fire on Marywilska Street in the capital.
"Due to evidence that the Russian special services committed a reprehensible act of sabotage against the shopping centre on Marywilska Street, I have decided to withdraw my consent to the operation of the Consulate of the Russian Federation in Krakow," Foreign Minister Radoslaw Sikorski wrote on X.
Sikorski told reporters at a meeting of foreign ministers in London that Poland will take further action if attacks such as the one on the shopping centre continue.
Foreign ministry representatives said Russia would have about 30 days to close the Krakow consulate, which employs three diplomats and four other employees.
The Russian foreign ministry said Poland was cutting its ties with Moscow on purpose, state news agency RIA reported.
"Warsaw continues to deliberately destroy relations, acting against the interests of its citizens," state news agency RIA quoted Russian Foreign Ministry spokeswoman Maria Zakharova as saying.
Russia would soon deliver an "adequate response", she said.
In October, Poland announced it would shut down the Russian consulate in Poznan due to suspected Russian attempts at sabotage.
Russia closed the Polish consulate in St Petersburg in response.
As well as Krakow and Poznan, Russia has a consulate in Gdansk and its embassy in Warsaw.
In March, Lithuanian prosecutors accused Russia's military intelligence of orchestrating an arson attack on an IKEA store in Vilnius, which broke out three days before the shopping centre fire in neighbouring Poland.
Russia has denied involvement in the arson attacks.
with Reuters
