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Labour MP: Office security 'breached' by leaders' staff
Ms Malhotra, who resigned as shadow chief secretary to the Treasury last month in protest at Mr Corbyn's leadership, said there had been unauthorised access to her office "on more than one occasion".
She said she had "no idea" who went in and why, saying the incident raised "fundamental questions" about the "security and safety" of her staff.
In her letter to Commons Speaker John Bercow, she said her staff had felt "harassed, intimidated and insecure".
Speaking on the Andrew Marr Show, Mr McDonnell - who had been Ms Malhotra's boss in Labour's Treasury team - said his office manager had spotted a pile of boxes outside her office a month after she resigned and assumed that office was empty.
He said the member of staff, who was worried about losing her job, had apologised to Ms Malhotra's team and that he had not been told before the formal complaint to Mr Bercow was lodged.
Turning directly to the camera in his BBC interview, he appealed to the party to "stop this now".
"There's a small group out there that are willing to destroy our party just to remove Jeremy Corbyn," he said.
It was "fine" for them to target the leadership, he said, "but don't pick on staff who can't defend themselves".
Mr McDonnell predicted that Labour MPs would accept the result if Mr Corbyn retained the leadership, saying most of them "just want to get on with the job".
He also acknowledged he and Mr Corbyn had made mistakes in their Labour leadership and said they would resign if Labour lost the next general election.
Ms Malhotra's replacement as shadow chief secretary, Rebecca Long-Bailey, told Sky News staff had been planning to swap their offices and thought Ms Malhotra had already vacated hers.
On realising Ms Malhotra was still based there, the member of staff "walked straight back out of the office again and left", Ms Long-Bailey said.
She added: "Unfortunately there has been a bit of miscommunication and misunderstanding on both sides."
Speaking on Saturday, Mr Corbyn condemned abuse among members, saying "it has no place in our party".
He said: "I don't do personal abuse, I don't respond to personal abuse, I condemn any abuse from others."
Mr Smith - the former shadow work and pensions secretary - said the party was on "its knees" and could split if Mr Corbyn remained at the helm.
He told Sky News: "We are not looking at the moment like a government-in-waiting. We don't look like a credible powerful opposition, one that people could imagine running the country. I think that's what we've got to be."
Mr Smith has also said his wife, Liz, had been a victim of online abuse and claimed there was now a level of abuse, anti-Semitism and misogyny in Labour that was not there before Mr Corbyn became leader.
"My wife stood recently for a community councillor position in the village where we live in South Wales and was subject to a torrent of online abuse. It's a community council position."
He added: "I think it's just absolutely unacceptable."
The winner of the leadership contest will be announced on 24 September.