Almost 2000 people have signed a petition urging David Meikle to resign over what they called a "shameful" stunt.
Mr Meikle, councillor for Pollokshields, waved the Israeli flag as civic leaders raised the Palestinian flag over the council HQ on Friday. The city said it was to show solidarity with those affected by the conflict in Gaza.
Jewish communities reacted angrily to the raising of the Palestinian flag and said it would only stir up tensions and cause "offence and division".
Mr Meikle accused council leaders of failing to condemn the actions of Hamas, the Islamic terrorist group that rules Gaza.
However, hundreds of people criticised his decision to wave the Israeli flag and the petition has already attracted more than 1700 signatures.
It reads: "He has shown no regard to the views and feelings of his constituents.
"He is entitled to his beliefs and opinions. But because of his unprofessional conduct, the place and the timing of his expression leads us to believe he can no longer represent us and should therefore resign immediately."
Meanwhile, a second online petition, organised by campaigner Donald Lawrie and which has been signed by more than 600 people, is calling for the council to pledge not to fly the Palestinian flag from the Chambers again.