The Aussie musician stated he "loved Israel" during a recent media conference and vowed to continue to play concerts in Tel Aviv, despite pressure from various artists to cancel them.
In response to Cave's remarks on Sunday, Waters said, "Nick thinks this is about censorship of his music? It is a political and moral decision to stand with the oppressor against the oppressed".
"No one wants to be publicly shamed", he said.
The Australian artist, known for music that can be both melancholic and uplifting, is popular in Israel and is set to perform a pair of almost sold-out shows.
In 2013, the Anti-Defamation League, having previously defended Waters against charges of anti-Semitism, acknowledged that "anti-Semitic conspiracy theories" have "seeped into the totality" of the former Pink Floyd frontman's views.
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"I admire Nick Cave as an artist and I know he has been generous in his support for Palestinian humanitarian causes".
He noted an affinity to Israel. "So really, you could say, in a way, that the BDS made me play Israel".
But the band ignored the call to boycott, with Thom Yorke telling Rolling Stone magazine that it was "deeply distressing" that Waters and other BDS activists "choose to, rather than engage with us personally, throw s**t at us in public". And that just seemed to me cowardly, really.
Cave had said that Eno was directly responsible for his decision to play in Tel Aviv. "I don't like lists", he said.
Cave told the story of how a few years ago, British musician Brian Eno tried to urge him to sign an artist's petition by an organization called "Artists For Palestine" to boycott Israel.
He continued: "After a lot of thought and consideration, I rang up my people and said, 'We're doing a European tour and Israel.' Because it suddenly became very important to make a stand against those people who are trying to shut down musicians, to bully musicians, to censor musicians, and to silence musicians".
Earlier this month Boy George, the lead singer of Culture Club performed in Tel Aviv with his band saying "I go where I want", and would not listen to those pressuring him to boycott Israel. I didn't connect to it.