Sir Gavin Williamson has been accused of sending "threatening messages” to a female Tory MP.
The complaint from Wendy Morton, the former chief whip, is being investigated by Conservative Campaign Headquarters (CCHQ).
Sir Gavin, who was brought back into cabinet by the Prime Minister in last week’s reshuffle, has denied the claims.
Labour said the “revelations raise fresh questions about Rishi Sunak’s woeful judgment.”
The allegations were first reported by the media organisation Tortoise, and concern "vile and threatening messages” supposedly sent by Sir Gavin to Ms Morton in the days leading up to the resignation of Liz Truss.
One MP told Tortoise that the submission to CCHQ included screen grabs of messages.
He said there was “quite a bit of evidence”, and that a number of MPs were willing to back Ms Morton up.
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A Conservative Party spokesperson said the party had “a robust complaints process in place.”
A friend of Sir Gavin said he “strongly refutes these allegations” and is “very happy to share all communications with the former chief whip with CCHQ if needed”.
Sir Gavin has been already been sacked from government twice.
He was forced out as defence secretary when a Cabinet Office investigation concluded he had leaked confidential information about Huawei from the National Security Council.
He later quit as education secretary following the pandemic exams debacle.
Labour’s deputy leader Angela Rayner said: "These new revelations raise fresh questions about Rishi Sunak’s woeful judgment in resurrecting ministers who left Government under a cloud of misconduct.
“Gavin Williamson was sacked from Cabinet twice, yet despite risking national security he has now been put at the heart of the Government’s corporate headquarters.
"Given his new role and the seriousness of these allegations, there must be an urgent and independent investigation.
"Far from restoring integrity, professionalism, and accountability, Rishi Sunak is failing to stop the rot.
"He promised that appointing an independent ethics adviser would be one of the first things he would do as Prime Minister, but instead he has given us more of the same old sleaze."
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