Zack Polanski has said he will not accept anyone being excluded from the Green Party "because of the religious or communal body they are part of", after members adopted a motion declaring Zionism a form of racism.
The Green leader said "no-one will be made unwelcome because of their background, their faith, or where they worship".
The motion defines Zionism as an ideology supporting "an ethnonationalist Jewish state" and backs a "single democratic Palestinian state in all of historic Palestine".
More than a dozen Labour MPs reported the Greens to the equality watchdog on Monday, saying it raised "serious questions".
A Green Party spokesperson said: "We remain committed to upholding our own Code of Conduct and our duties under the Equality Act, and to ensuring the Green Party continues to be a safe place for all members."
Nine Labour MPs have also referred the party to Sussex Police, asking the force to investigate whether alleged "possible antisemitic offences" at the conference merit a criminal investigation.
Sussex Police has been contacted for comment.
It is the latest development in a backlash to the policy motion, which was put forward by a group of activists at the party's conference in Brighton and endorsed by 1,022 votes to 813.
"The real, material, manifestation of Zionism has been the historic and ongoing dehumanisation, displacement, dispossession, disenfranchisement and destruction of Palestinians," it said.
The motion has exposed divisions between the party's newly enlarged membership base under leader Zack Polanski and its MPs elected at the last general election.
Polanski did not take part in the vote on Sunday and four of the party's five MPs opposed it.
Israel's foreign ministry responded by banning Polanski from entering the country, while some Jewish groups have described it as an "attack on the Jewish community".
In his first comments since the motion was passed, having declined interviews on Monday, Polanski released a lengthy statement saying he "take[s] seriously my responsibility to make sure everyone feels safe and welcome in our party".
He added: "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 said his party and its leadership stood for "deeply held values of compassion, fairness and equality for all".
Polanski, who is Jewish, added that "antisemitism and criticism of the Israeli state are, and must always be, completely distinct".
On Monday, a group of Labour MPs wrote two letters to the Equality and Human Rights Commission (EHRC) - organised by former Home Office minister Mike Tapp - raising concerns about the motion, and amendments to protect Jewish members attending Zionist synagogues being voted down.
"Taken together, these developments raise serious questions about whether Jewish members can participate freely and equally in the party, and whether their religious and communal connections could expose them to complaints or disciplinary action," their letter to the watchdog said.
The EHRC, which regulates equality law in Great Britain, previously found failings in how Labour handled antisemitism.
In a statement, the EHRC told the BBC it would "consider each complaint carefully" and had not at this stage launched an investigation.
It added: "We have guidance advising political parties on their responsibilities under the Equality Act 2010. Like all duty-bearers, political parties must comply with the Act and take steps to avoid discrimination."
The European Green Party, of which the Green Party for England and Wales is a member, released a statement on Monday saying it wanted to "unequivocally distance" itself from the motion.
The umbrella body said it would "immediately demand clarity" from the party's leadership on how they would protect Jewish people and self-determination.
Meanwhile, Green MP Ellie Chowns told Radio 4's PM programme she was "deeply saddened" the motion had become party policy but disagreed it was antisemitic, saying it was underpinned by "principled opposition to the actions of the Israeli government".
She suggested a review of Green policymaking processes was needed since "less than 1%" of the party's more than 200,000 members had participated in the vote.
