The English and Welsh Greens are facing international ostracism after adopting a policy declaring Zionism as a form of racism, which has drawn dismay from the group representing European Greens.

The co-leader of the German Greens separately said the policy was "intolerable and unacceptable", running contrary to its belief in the right of Israel to exist.

The binding policy motion passed in a vote at the Greens' conference in Brighton on Sunday. Four of the party's five MPs opposed it.

The policy says Zionism, the movement for a Jewish state, should be "treated as any other form of racism", and backs a single democratic Palestinian state across historic Palestine "with equal rights for all".

The European Green party, which represents 47 parties, including the Green party of England and Wales (GPEW), said it supported a two-state solution for Israel and Palestine, and the new motion went against this.

The alliance "will immediately demand clarity from the leadership and parliamentary group of GPEW, to understand the official party policy of GPEW, how they position themselves towards the self-determination of Israelis and Jews as well as the protection of Jewish people and members in the party", it said in a statement.

Felix Banaszak, the leader of the German Greens, known formally as Alliance 90/the Greens, told a press conference the motion was "intolerable and unacceptable".

"It runs counter to everything that Alliance 90/the Greens stands for in Germany, and it also runs counter to what the European Green party stands for," he added.

Banaszak said: "There is a widely held view within the European Green party that Israel has a right to exist and that this right must not be undermined." His party would "approach our partner parties in Europe to clarify how to deal with this".

Sandy Ruthven, the chair of Amnesty International UK's charitable trust and a longstanding Green member, resigned over the motion and accused the party of failing to confront antisemitism.

The fallout from Sunday's vote has also intensified a debate over whether the Greens' highly decentralised policymaking structures remain suitable for a party whose membership has expanded rapidly.

Policy is made at the party's two annual conferences, which generally involve a small proportion of members. The Zionism motion won just over 1,000 votes, approximately 0.4% of the total membership.

Ellie Chowns, a former co-leader, said the party's governance and policymaking "urgently need to be modernised".

"As a party we pride ourselves on our democratic member-led policymaking process, but I do think we need to ask ourselves some searching questions when less than 1% of our members actually participate," Chowns, the Green MP for North Herefordshire, told the Guardian. "This is long overdue and has become even more urgent with the huge expansion of our membership."

Chowns said she understood the concerns of European Greens, which she shared, but stressed: "There is still much more that unites us than divides us."

One source in the party said the criticism from European Greens, especially those in Germany, was understandable given their differing stances on Gaza and Israel.

They said: "The German Greens support arming Israel, opposed a ceasefire to Israel's onslaught on Gaza, backed the suspension of funding to Unrwa and co-sponsored a Bundestag resolution describing the arguments and methods of the peaceful, Palestinian-led BDS campaign as antisemitic."

Any change to internal party structures would be hard to implement. One Green insider said that to give MPs greater authority over members would undermine the party's commitment to grassroots democracy. However, they said the existing model could produce a lack of coherence and strategic direction, while giving a disproportionate influence to members with the most time to participate in policymaking.

They suggested members could determine broad strategic priorities, with smaller bodies developing detailed policy while remaining accountable to the membership.

Another senior Green defended the party's model of direct democracy, arguing that allowing members to determine policy was fundamental to the party's character.

Daniel Schuster, the regional director of the Simon Wiesenthal Center's European office, said: "The British Green party's decision to formally classify Zionism as a form of racism is absurd, not based on any logical basis and is itself racist. And timing, just days before the third anniversary of the 7 October terrorist Hamas attacks, is designed to inflict pain on a deeply solemn occasion.

"Branding Zionism itself as racism crosses a profoundly consequential line. It takes a movement for Jewish national self-determination and transforms it into something for which Jews are expected to apologise. We will not."

In a statement, the Green party leader in England and Wales, Zack Polanski, said: "Antisemitism and criticism of the Israeli state are, and must always be, completely distinct – blurring the line between the two is not only wrong but antisemitic, and makes Jewish people less safe. It's our role as a movement for justice to protect both the rights of Palestinians and our Jewish communities here in the UK. As leader I will not accept any exclusion, or refusal to engage with anyone, because of the religious or communal body they are part of."

He added: "Through the Green party's unified stance and dedicated pressure, we have begun to shift this government away from its complicity with the Israeli government's atrocities in Gaza, with the foreign secretary now taking the long overdue step of ending trade with illegal settlements."