Zack Polanski has said he would not have voted for a motion passed by Green Party members declaring Zionism a form of racism.
The Green Party leader told BBC Breakfast the motion was "imperfect" and he would have voted for an amended version.
However, he said the "substantial part of the motion", that "the displacement and genocide of the Palestinian people is clearly underpinned by a racist ideology" was "obvious". Israel has repeatedly denied its actions in Gaza amount to genocide.
The motion defined Zionism as an ideology supporting "an ethnonationalist Jewish state" and backed a "single democratic Palestinian state in all of historic Palestine", which includes modern-day Israel.
Polanski has faced criticism - including from some senior Green Party figures - over his response to the motion.
He is facing further questions over his leadership, after he finished second behind Labour in the Holborn and St Pancras by-election.
Speaking after the result, Polanski insisted he would stay on as leader, telling broadcasters: "Yes I've taken a loss tonight but our movement is so much bigger than one election or one motion."
Polanski did not take part in the debate or vote on the motion at the Green Party's annual conference in Brighton on Sunday, instead leaving the conference early to campaign in Holborn and St Pancras.
Until Friday morning, he had not explicitly said whether he would have voted for the motion and had declined media interviews in the final days of the by-election campaign.
Under Green Party rules, motions supported by members become official party policy, but will not necessarily be included in the party's manifesto at the next general election.
In an interview with BBC Breakfast, Polanski was asked repeatedly how he would have voted if he had been present.
"There's parts [of the motion] I disagree with and parts I agree with," he said.
"The part I disagree with is the Green Party of England and Wales or indeed even the British government deciding that there should be a single state. I think that's up to the Israelis and the Palestinians."
Polanski, who is Jewish, added: "In terms of the actual substantial part of the motion... the displacement and genocide of the Palestinian people is clearly underpinned by a racist ideology. I think that's obvious."
Several UN reports have accused the Israeli government of committing war crimes which amount to genocide in Gaza. Israel has repeatedly denied all such allegations.
On Friday morning, following the Zionism row, Polanski was asked repeatedly on BBC Radio 4's Today programme whether he believes Israel has a right to exist.
"I don't believe any state has the right to oppress or to commit apartheid and certainly not genocide on another people," he said, adding: "I don't believe that's a state that anyone should be supporting."
Asked by presenter Nick Robinson for a "yes/no" answer on this question, he said: "I've repeated many times that I want to see equal rights for Israelis and Palestinians - at the moment Palestinians don't have equal rights so I think I'm answering your question really clearly."
Pressed on BBC Breakfast over how he would have voted in the motion had he attended the conference, Polanski said he would have supported amendments, "including to make sure that we weren't determining there was a single democratic state".
He added: "The motion as amended, I would have voted for. The motion unamended, I wouldn't have voted for."
Polanski has also previously said he wanted to see the motion amended to specify that it should not be used to discipline Jewish members attending synagogues that consider themselves Zionist.
However, both amendments favoured by Polanski were rejected by Green members.
Polanski has sought to reassure Jewish members by saying nobody will be excluded from the party on the basis of their faith, where they worship or the religious body they are part of.
However, groups including the Jewish Leadership Council and the Board of Deputies of British Jews have condemned the motion, branding it an attack on the Jewish community.
Polanski has also faced criticism from former Green Party leader Caroline Lucas, who told BBC Newsnight he had failed to show leadership over the motion, which she described as "dangerous", "divisive" and "flawed from top to bottom".
Her comments came shortly after polls closed in the by-election but before the result was declared.
Asked if Polanski should stand down, she told the programme: "I think let's just see what happens in the coming days and weeks. Obviously he has been completely taken up with this by-election.
"I want him to speak now about what's happened, I want him to show the leadership that was frankly missing on Sunday.
"I think the jury is out about whether he will do that - but I very much hope he will."
Responding to Lucas's criticism, Polanski told the BBC "I like and respect Caroline a lot" and "she's entitled to her opinion".
However, he added: "The reason why I wasn't at the conference debate is because there was a national by-election."
The motion overshadowed the final days of Polanski's by-election campaign, where the Greens had been hoping to overturn a substantial Labour majority in the seat vacated by former Prime Minister Sir Keir Starmer.
Although Polanski lost out to Labour's Sagal Abdi-Wali, the party saw its majority reduced from 11,572 to 3,364.
The motion has sparked days of controversy and exposed divisions between the Green Party's newly enlarged membership base under Polanski and its MPs elected at the last general election.
Four of the five Green MPs opposed the motion, while the party's co-deputy leaders were split over whether they supported it.
The vote also led to the resignation of the Green deputy leader in Wales and condemnation from the European Green Party.
Meanwhile, Prime Minister Andy Burnham called on Polanski to reverse the motion and ensure it is not Green Party policy.
In his first comment on the row on Thursday, Burnham said it was "completely wrong" for the party to support the motion and this showed "terrible judgement".
The PM said he felt the motion effectively ruled out a two-state solution between Israel and Palestine.
"For that reason, it shouldn't be supported in any way, shape or form," he told reporters while on a visit to Berlin.
