Local Green Party of England and Wales representatives had been given an ultimatum by Labour to disown the policy or face the collapse of coalition agreements.
Labour chair Bridget Phillipson said local deals “cannot come at the expense of upholding the moral obligation we have” to stand up for all parts of the community.
Co-operation will be or already has been withdrawn in: Arun District Council, Derbyshire Dales District Council, Havant Borough Council, Lewes District Council, Runnymede Borough Council, Sheffield City Council, Stafford Borough Council, Warwick District Council, Wealden District Council, West Devon Borough Council and West Suffolk Council.
In Coventry City Council there was no formal arrangement in place and no formal arrangement will be made in future.
Co-operation will continue in Broadland District Council, Monmouthshire County Council, North Somerset Council, Rother District Council, West Oxfordshire District Council and West Sussex County Council.
Co-operation will also continue in the West of England combined authority, where Labour mayor Helen Goodwin has a Green deputy.
Ms Phillipson said: “The Labour Party exists to deliver for communities across the country at all levels of government.
“Any local powersharing arrangement cannot come at the expense of upholding the moral obligation we have to stand up for everyone in our communities and the values we share.
“Labour has been clear from the start that the ‘Zionism is racism’ policy crosses a line and we cannot work with any party that supports it – at any level of government.”
The Green Party and its Local Government Association group representing councillors condemned Labour’s move, warning it would cause disruption at the affected authorities.
In a statement, they said: “Across the country, Green, Labour, Independent and Liberal Democrat councillors have worked together to provide stable local government, protect services and deliver positive change. Leaders across these parties are rightly proud of what those partnerships have achieved.
“Those who issued ultimatums that destabilised powersharing agreements have often ignored the judgments of their own local leaders, failed to respect the choices made by local voters, and are disrupting successful partnerships.”
The statement said: “The Green Party believes top-down directives to break up and disrupt locally run services are not in the interests of the residents we represent.
“We trust local communities, local councillors and local leaders to know what is best for them. We ask that others do the same.”
The row follows members at the Green Party’s conference passing an anti-Zionist motion which has led to condemnation from political opponents and the Board of Deputies of British Jews.
The motion declared the Greens to be an “anti-Zionist party” and sets into its policy that Zionism, the movement to develop and protect a Jewish state in Israel, will be “treated as any other form of racism”.
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