Bridget Phillipson has told Labour groups in joint local administrations with the Greens to review their agreements and seek a clear rejection of the Greens' "Zionism is racism" policy.
Local Green groups have been given seven days to provide what Labour describes as an unambiguous statement condemning the motion and calling on their national leadership to reconsider it.
Phillipson said Labour would end a local power-sharing arrangement where that assurance was not provided. Reports indicate that the instruction affects 19 councils, although the legal and political form of those arrangements varies between areas.
The Green motion was adopted at the party's conference this month by 1,022 votes to 813. It equates Zionism with racism, rejects a two-state solution and supports a single Palestinian state with equal rights for all.
Prime Minister and Labour leader Andy Burnham described the motion as antisemitic and ruled out a partnership with a party holding that position. The Equality and Human Rights Commission has asked the Green Party for information so it can assess the motion's practical implications.
Individual Green groups can distance themselves from the national policy without facing automatic party discipline. Some local groups have already rejected it, meaning the Labour instruction does not itself end every existing arrangement immediately.
Phillipson is Labour chair and Minister for Women and Equalities. Her intervention moves the dispute from national rhetoric to a deadline with potential consequences for council administrations.
