Cllr Laurence Lavigne Lalonde explained to the city's executive committee meeting that the crucifix would be removed before scheduled renovation work at City Hall.
However, Lalonde said it would not be put back in the chamber when City Hall reopens.
"I think we can agree the context has changed today," Lalonde said, noting that the crucifix was put on display above the main door of the council chamber in 1937 to remind councillors of the oath before God that they took.
Successive governments have rejected requests to remove the Christian symbol.
Last October, the Coalition government argued the crucifix was an important part of Quebec's heritage.
The debate comes as the government moves to impose strict religious neutrality rules on state employees in positions of authority.
If passed, workers such as teachers, judges and police officers would be forbidden from wearing visible religious symbols.
"The City of Montreal has the power to take down the crucifix," Immigration, Diversity and Inclusiveness Minister Simon Jolin-Barrette told local reporters on Wednesday in Quebec City.
"The national assembly has always decided to maintain it, and that's the position of the government, because it's a patrimonial symbol."
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