The musician who previously blamed Ukraine for the war and criticised the West's support canceled the concerts without giving any reason, local media reported.
An official with the Tauron Arena in Krakow, where Waters was scheduled to perform two concerts in April, said they would no longer take place.
The website for Waters' This Is Not a Drill concert tour did not list the Krakow concerts previously scheduled for April 21-22.
City councillors in Krakow were expected to vote next week on a proposal to name Waters as a persona non grata, expressing indignation over the musician's stance on the war in Ukraine.
Waters wrote an open letter to Ukrainian first lady Olena Zelenska early this month in which he blamed extreme nationalists in Ukraine for having set your country on the path to this disastrous war.
He also criticized the West for supplying Ukraine with weapons, blaming Washington in particular.
Waters has also criticized NATO, accusing it of provoking Russia.
Waters was not involved in Pink Floyd's song that was made after the group was moved about the situation in war-torn Ukraine.
The song Hey Hey Rise Up, released in April, was the band's first music since 1994 and was made in protest of Putin's invasion.
Waters officially left the band in 1985, which put a strain on his relationships with the remaining members, but he eventually reunited with them in 2005 for a set in London's Hyde Park.
