A recording leaked to the Sunday Times reveals Mr McDonnell said: “I’ve just seen some of the scale of the abuse that she’s been getting...
"I’m hoping one day that people will see what she’s had to go through in terms of the vile comments that have been made about her.”
The LRC, a left-wing pressure group within Labour, has previously described allegations of antisemitism “ruling class propaganda”.
Mr McDonnell is its honorary president.
Marie van der Zyl, the president of the Board of Deputies, accused him of “double-speak” in condemning antisemitism in public but defending Jackie Walker, adding he has “proven he has no honesty or integrity”.
A spokesman said: “If Jeremy Corbyn does nothing about this then he too is complicit.”
Ms Walker attended the LRC conference on Saturday, where she repeated claims that accusations of antisemitism are an attempt to undermine the party’s leadership, the Sunday Times reports.
She went on to say that Labour MPs leading the fight against antisemitism, including Luciana Berger, were “untouchable”, asking why the leadership had failed to “censure” them.
Ms Berger was due to face a motion of no-confidence by members of her constituency Labour Party (CLP) but it was dropped amid outrage from senior party figures, including Yvette Cooper and Ed Miliband.
The two motions against Ms Berger, the parliamentary chair of the Jewish Labour Movement, condemned her vocal criticism of Mr Corbyn and the party leadership for failing to tackle antisemitism.
On Sunday, Tony Blair accused the current leadership of not being “robust” enough on antisemitism, coming to the defence of Ms Berger.
Speaking on Sky’s Sophy Ridge on Sunday, he said: “We’re supposed to be a progressive political party.
“How can we say it’s tolerable to have a certain level of antisemitism in the party? Would we say more generally it’s tolerable to have a level of racism in the Labour Party? No, of course you can’t.
“[The leadership] has not been robust enough on it, and the fact that someone like Luciana Berger, who’s a smart, capable, active member of Parliament doing a her best for her constituents, the fact that she should even be subject to a confidence motion is shameful for the Labour Party.”
The former Prime Minister also backed calls by the deputy leader Tom Watson for the Liverpool Wavertree CLP to be suspended over the proposed motions.
The JC has learned that neither Mr Corbyn nor Ms Formby will present a report on disciplinary proceedings related to antisemitism at this week’s Parliamentary Labour Party meeting, as demanded in an 11-point motion passed by MPs this week.
A Labour spokesman said: “The Labour Party is committed to tackling antisemitism in all its forms wherever it arises, in our Party and wider society.
“We have significantly sped up and strengthened our procedures for dealing with complaints about antisemitism.”
