The flag was raised on the clock tower in a ceremony attended by President Andrzej Duda and First Lady Agata Kornhauser-Duda.
After the ceremony, the presidential couple handed out red-and-white flags to Warsaw residents.
The Polish Prime Minister's Office said in a tweet that "the white and red flag is one of our most important national symbols," with the white representing "goodness and purity," and the red standing for "love and sacrifice."
Later in the day, Defence Minister Mariusz Błaszczak led a military event at Warsaw's central Piłsudski Square.
Polish Defence Minister Mariusz Błaszczak. Photo: PAP/Radek Pietruszka
Błaszczak said in a message that the Flag Day celebration aimed to promote "respect for the national colours and symbols."
Poland's Flag Day is a relatively new tradition that was established in 2004.
People across the country were being encouraged to display national flags in front of their homes.
Day of Poles Abroad
As well as Flag Day, May 2 is the Day of Poles Abroad, and Polish Foreign Minister Zbigniew Rau has sent his best wishes to his compatriots living in other countries.
May 2 marks Flag Day in Poland, when many people display the national red-and-white colours and are encouraged to make patriotic statements.
Meanwhile, May 3 is Constitution Day, celebrating a historic constitution the country adopted on May 3, 1791.
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Source: PAP