The new chief executive of the People’s Vote campaign has stepped down pending an investigation into allegations of harassment towards female staff.

Patrick Heneghan, who was appointed to the role two weeks ago, has been accused of inappropriate behaviour by three women who work at the campaign.

Female staffers wrote to the board of Open Britain, the largest organisation under the umbrella of People’s Vote, saying they felt “unsafe” returning to work while Mr Heneghan was in charge.

Members of the board, chaired by businessman Roland Rudd, have now been informed that Mr Heneghan will take a leave of absence while an investigation takes place, The Independent understands.

Complaints were handed to the board about Mr Heneghan’s conduct from three female staffers, who allege he asked them to come back to his flat, suggested taking cocaine and became “handsy” with some staff.

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In a joint letter, a group of 16 women wrote to the board: “Please don’t underestimate how awful a situation this is for us, as women, to be in.

“The complaints that have been voiced about Patrick Heneghan are such that none of us feel safe returning to work whilst he is in a position of power and authority.”

Mr Heneghan denied the claims, which he described as “politically motivated”.

The move comes amid bitter turmoil at the second referendum campaign after two senior figures were abruptly sacked in a “boardroom coup” and Mr Heneghan, a former Labour head of campaigns, was appointed.

In a email to the Open Britain board, seen by The Independent, fellow board member Anne Weyman said Mr Heneghan had agreed to step down while a probe is conducted.

It said: “I met yesterday with a number of female staff members of Open Britain ... Their main concern was that they did not feel safe working in the office while Patrick Heneghan was there.”

Ms Weyman continued: “At the outset of the investigation into the allegations against Patrick, we took the decision that the investigation could be undertaken with him remaining in post.

“Roland [Rudd] has spoken to Patrick, who has, with a heavy heart, come to the same conclusion.

“He also believes that the best thing, now, is for him to take a leave of absence for the period of the investigation, and is determined to clear his name.”

Mr Heneghan said: “I totally deny these politically motivated allegations. I have already complied with the initial investigation and will now take a couple of weeks leave to comply with another one.”

Stuart Hand, who was a director of campaigns at Open Britain, has been appointed as his replacement.

A group of People’s Vote campaign staff said in a statement: “Almost two weeks since Roland Rudd, the chair of Finsbury Lobbying, took a wrecking ball to the best political campaign in the UK, the person he imposed as acting CEO has been suspended.

“This decision will at least allow women, who warned the Open Britain board that Patrick Heneghan’s presence represented an unsafe working environment, the chance to re-enter the office.”

However they criticised the board for failing to consult with some of the organisations involved, and warned that there was a “real danger that the errors of the past fortnight” will be repeated.

People’s Vote declined to comment.

It comes after a number of turbulent weeks for the campaign which has seen staff members pass a motion of no confidence in Mr Rudd, the chairman of Open Britain.