Dürr died suddenly on Thursday at the age of 46, Polish state news agency PAP reported, citing the Czech foreign ministry.
In November last year, he took sick leave and returned to Prague from Warsaw, according to officials.
Polish Prime Minister Mateusz Morawiecki said in a Twitter message on Thursday: "I am deeply saddened by the news of the death of Jakub Dürr, the Czech ambassador to Poland."
Morawiecki added: "A great diplomat, he worked hard for Polish-Czech relations. He passed away so suddenly, at such a young age... My deepest condolences to his family and friends. R.I.P."
Polish Foreign Minister Zbigniew Rau said in a tweet: "It was with great sadness that I received the news of the sudden death of the Czech Ambassador to Poland, H.E. Jakub Dürr."
He added: "Just a few days ago we celebrated together the 30th anniversary of Poland and the Czech Republic establishing diplomatic relations."
Rau also said that Dürr "will be remembered as a highly professional diplomat and a kind man who contributed to strengthening Polish-Czech relations."
The Polish foreign minister offered his "condolences to the ambassador's family and loved ones."
The Czech embassy in Warsaw said Dürr was "an excellent diplomat and a great expert and friend of Poland."
Czech Prime Minister Petr Fiala also offered his sympathies in a Twitter post.
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Source: IAR, PAP