In a letter to Commons Speaker John Bercow, Ms Malhotra, former shadow chief secretary to the Treasury, also claimed her “privacy, security and confidentiality” had been violated after a member of shadow chancellor John McDonnell’s team gained entry to her office.
However, a Labour party source told Sky News: "Seema has two offices and is basically squatting in the office and refusing to move. It's malicious and so is her letter."
The controversy comes amid a bitter civil war within the Labour party between supporters and opponents of Mr Corbyn, who is facing a leadership challenge from MP Owen Smith.
The letter said the unnamed Corbyn aide accessed the room with a key card on 15 July, when Ms Malhotra was at a constituency meeting.
The aide was said to have been “surprised” to find a member of Ms Malhotra’s staff on the premises and, when asked why she was there, said she was “just being nosey”.
The letter said Ms Malhotra was unclear what the aide's "intentions were".
"She kept referring to my staff as 'girls', which made them feel insulted and patronised, and said that 'she had people waiting to use the office'.
"These incidents have frightened my staff, including a new intern, who have become concerned about their safety and as such took the decision that no member of staff is to be left alone in the office.
"As this is a serious breach of Parliamentary privilege, I would be grateful if an urgent and thorough investigation is undertaken into the actions of these individuals and any other associated parties.
"I understand that [the Corbyn aide] has been in my office at least twice in recent weeks, when I have not been there, and was aggressive and intimidating. She would interrogate my staff, asking them questions about who worked in my office, what their roles were, and why we couldn't move out."
Only a police search warrant can justify entry to a Parliamentary office without the wishes of an MP, as agreed following the police search of MP Damian Green’s offices in 2008.
It is believed Ms Malhotra has also written to Labour’s general secretary, Iain McNicol, to demand an internal investigation into the matter.
Mr McDonnell responded by saying there had been a misunderstanding and there were no nefarious reasons behind the aide’s entry into the office.
“I find this really distressing. We thought she had moved out of her office; my office manager saw boxes outside her office and thought she had moved,” he said, speaking on the Andrew Marr Show.
“I've got a member of staff ... she's now worried she's going to lose her job and face prosecution because it's been described as a break-in. That's just so distressing – it's unacceptable.
“Seema didn’t contact me before she wrote to the speaker; I got a copy of the email on Friday night. We thought she had moved out. I don’t know what’s going on.”
Ms Malhotra resigned as shadow Treasury secretary on 26 June, saying she had become concerned by the “growing divisions” within the Labour party.
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