Abe, 67, the longest-serving leader of modern Japan, was gunned down on Friday at a political rally in the city of Nara.
"A great leader of Japan and wonderful friend of Poland has passed away today," Duda wrote on Twitter.
"We are all shocked by the brutal murder of the former Prime Minister of Japan, Shinzo Abe," the Polish president added.
"I mourn along with his family, his friends and all the people of Japan. My thoughts and prayers are with you," Duda wrote.
Japan has some of the tightest gun control laws in the world, but they failed to prevent the 41-year-old gunman from shooting Abe with a home-made gun. The attacker, identified as Tetsuya Yamagami, used to serve in Japan's Maritime Self-Defence Forces. (PAP)
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