Waverley Council's Ludovico Fabiano attempted to amend a motion about the Israel-Gaza conflict to call out "war crimes" by Israel but was voted out of his position during a public meeting on Thursday evening.
The council, which represents the state's largest Jewish community in Sydney's east, voted on a motion last week to condemn the attack on Israeli civilians by Hamas.
Mr Fabiano said he could not commit his full support to the motion as it failed to mention any attacks on civilians in Gaza.
Together with fellow Greens councillor Dominic Wy Kanak, the pair attempted to amend the motion to condemn both Hamas and Israeli attacks.
The amended motion proposed to condemn "war crimes perpetrated by Hamas, including the premeditated targeting of Israeli civilian" as well as to condemn "war crimes perpetrated by a right-wing Israeli government including the bombing of Palestinian civilians".
The amendments were voted against by all other council members and prompted a petition calling on Mr Fabiano to be sacked.
His stance caused "significant distress and disappointment" Change.org campaigner and former Zionist Council of NSW director Daniel Rod said.
"Equivocating the actions of HAMAS with those of Israel, especially during such a sensitive time, is unacceptable and shows a lack of understanding and empathy."
During an extraordinary meeting on Thursday night, Mr Fabiano was voted out of his position.
The former deputy mayor said he was surprised and "deeply disappointed".
"Democracy took a step backwards in Waverley," he said.
"My crime? Wanting to include in our amendments to the Israel/Gaza motion a recognition of the trauma caused to the civilians of Gaza at the hands of the Israeli military."
Mr Fabiano said his views had been "misrepresented so badly as to describe the exact opposite of those I have expressed".
He also claimed to have received hateful and threatening emails and social media posts.
President of the NSW Council for Civil Liberties Lydia Shelly said shutting down dissenting views as an undemocratic abuse of power.
"This motion signifies a very concerning slide towards silencing those whose views may not conform with those who wield political power," she said.
Waverley council mayor Paula Masselos said Mr Fabiano wasn't removed over the amendment, but because he had lost the confidence of the community.
"It was absolutely a loss of confidence," she told ABC Radio on Friday.
"At the end of the day we are there as representatives of our local community.
"As leaders we're meant to be working for our community and looking for unity and resilience and not being provocative."
On the other side of the city, the Canterbury-Bankstown council in Sydney's west, agreed to fly the Palestinian flag over official sites until a ceasefire was called in Gaza.
Cabinet minister Tony Burke said Australians needed to distinguish between Hamas and Palestinians and allow those with connections to either side of the violence to grieve.
"There have been too many occasions where the two have been conflated and the military conflict is meant to be against Hamas," he told ABC Radio on Friday.
Mr Fabiano, who lost his position as deputy mayor but remains a councillor, said he will continue to "advocate for peace with justice".
"Peace comes from dialogue not bullets," he said.
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