A Labour MP has accused John McDonnell of "letting his allies go after" Luciana Berger after a row erupted over her future in the party.
Ms Berger is facing a vote of no confidence from local members for criticising Jeremy Corbyn.
Shadow chancellor Mr McDonnell said she should reject claims she supported a "breakaway party" to show members she was "sticking with Labour".
But Nottingham East MP Chris Leslie said his response was "ridiculous".
Labour's deputy leader Tom Watson also backed Ms Berger, telling the Commons she had "our solidarity and... our support as she battles the bullying hatred from members of her own local party".
And Labour MP Ian Austin - who faced suspension after a row over the party's anti-Semitism code - told PoliticsHome: "It's like something out of the Soviet Union's show trials where people were let off if they confessed their disloyalty and shouted 'Long Live Stalin'."
Ms Berger - an outspoken critic of the party's handling of anti-Semitism allegations and its stance on Brexit - said she would be not be "distracted from fighting for the interests of my constituents".
An extraordinary meeting has been called in the Liverpool Wavertree constituency next week to discuss two no confidence motions.
The motions accuse Ms Berger of being against Mr Corbyn, saying: "Instead of fighting for a Labour government, our MP is continually using the media to criticise the man we all want to be prime minister."
Votes of no confidence carry no official force within the Labour Party, but local activists could hold a "trigger ballot", where sitting Labour MPs can be forced to compete for selection as a candidate against all-comers, ahead of the next general election.
Ms Berger has been the target of online abuse and had a police escort at last year's Labour Party conference following death threats.
Earlier this week, she joined other MPs at a meeting of the Parliamentary Labour Party calling for details on the party's efforts to tackle anti-Semitism to be released.
In a statement, Ms Berger said she believed her constituents would judge her on her record and skills in representing them in Parliament.
She reiterated her "long-held view that Brexit will be a disaster for the people of Liverpool Wavertree and the wider country", saying she would "not shy away from standing up" for her Remain-voting constituency.
And she said she had made "no secret that, as a Jewish woman representing a city with a Jewish community, I have been deeply disturbed by the lack of response from Jeremy Corbyn as party leader and many in the wider leadership of the party to the anti-Semitism that stains our party".
Ms Berger added: "Nothing will deter me from exposing anti-Semitism wherever it festers, including in the Labour Party where it is being wilfully ignored."
Mr Leslie - a former shadow chancellor himself - told BBC Radio 4's World at One that Mr McDonnell had "demanded an oath of loyalty from her to those who are attacking her", adding: "I have never heard of such of a ridiculous situation.
"He should never have allowed his allies to have gone after Luciana like that in the first place. I have a feeling they will realise this is a terrible, terrible judgement."
Asked if he was considering whether to resign from the party, the MP did not rule it out, and said his "patience is wearing pretty thin" - namely around Labour's Brexit policy, as he supports a further referendum on whether to leave or remain in the EU.
He said had "serious worries" about the direction of the leadership of the party, adding: "Of course I have my issues with Jeremy Corbyn and the leadership, but the bigger point is there is a country and our constituents to put first here.
"If we keep getting told 'oh well get in line behind your party, shut up don't say anything, in fact, we're going to push you gradually out of the party for various reasons', don't expect us to just go quietly and say nothing. This is a serious moment."
A number of Labour MPs tweeted their support for Ms Berger after the news of the no confidence motions broke on Thursday night, including former leader Ed Miliband and prominent backbencher Yvette Cooper.
However, speaking to BBC Radio 4's Today programme, Mr McDonnell said the motion came about because Ms Berger is "associated" with rumours of a new centrist party being formed.
"[The motion] is an expression of views," he said.
"If people are doing that because Luciana has stood up against [anti-Semitism] that is completely wrong.
"But from what I have seen on social media, it looks as though what has happened is Luciana has been in the media associated with a breakaway party and hasn't been clear that she rejects that."
He condemned a Facebook post from one of the local Labour members calling Ms Berger a "disruptive Zionist", saying it was "completely wrong".
But the shadow chancellor said: "My advice to Luciana is just tell people you are not supporting a breakaway party, you are sticking with the Labour Party, you are not jumping ship.
"And my advice to the Labour Party members there is if there are differences of opinion there, get together, talk about it and see how you can support the campaign alongside your local MP."
Other Labour MPs criticised Mr McDonnell's response, with Chuka Umunna tweeting to shadow cabinet members: "Are we going to act? Defend a colleague in the face of this outrage?"
Ms Berger is not the first Labour MP to have faced a no confidence vote from their local parties over their views on Brexit. Others include Frank Field - who now represents Birkenhead as an independent MP - and Kate Hoey.
Conservative Nick Boles also believes his constituency party in Grantham and Stamford is looking to oust him as a candidate at the next election.
Meanwhile, Labour activists from the "Another Europe is Possible" group are targeting the constituencies of MPs who broke the whip and voted with the government over Theresa May's Brexit deal, calling it a "moment of reckoning".
Seven Labour MPs backed an amendment supported by the government calling for "alternative arrangements" to the backstop element of Mrs May's plan - which aims to avoid a hard border returning between Northern Ireland and Ireland.
And a total of 26 MPs either abstained or voted against an amendment by Yvette Cooper, which was backed by the Labour leadership, which would have allowed for an extension of Article 50 - the mechanism seeing the UK leave the EU on 29 March - by up to nine months, with the aim of avoiding a no-deal.
The left-wing group, founded last summer, will campaign in around 30 constituencies to "apply pressure" to the MPs to vote against Mrs May's deal.
Gordon Watson, the Labour deputy leader of Rotherham Council, warned that the rebels could end up facing de-selection if they don't vote the deal down, adding: "Failing to vote against the Tory deal is essentially propping up a government that is wrecking our communities. People are running out of patience."