Liz Truss accepted help during her leadership campaign from a former government minister accused of sexual harassment, No 10 sources claim.
The prime minister not only knew about the allegations, officials said, but suggested that he might make a return to serve in her government.
The politician, who denies any wrongdoing, initially tried to settle the matter informally with a letter of apology to the woman before reaching a financial settlement in the summer.
Claims of his links to Ms Truss come at the end of a difficult Tory conference for the prime minister and put further pressure on her refusal to appoint a parliamentary ethics adviser after Mr Johnson scrapped the role earlier this year.
She dismissed calls to do so, saying during her campaign that she knew the “difference between right and wrong”.
The Independent understands that the former minister provided some support behind the scenes for the Truss leadership campaign despite her being aware of the allegations, according to two No 10 officials.
She was among a clutch of cabinet members, including Mr Johnson, who were told informally of allegations, sources said. No formal investigation was carried out.
The ex-minister is alleged to have made inappropriate remarks to the civil servant, who subsequently complained. Senior officials reviewed the comments and decided that an investigation was not warranted.
The alleged victim was unable to turn to the Independent Complaints and Grievance Scheme (ICGS), which deals with incidents committed on the parliamentary estate — but not Whitehall or beyond. Civil servants can only access the ICGS if an incident took place on the estate and it involves a member of the parliamentary community.
After her efforts to secure an investigation proved unsuccessful, the alleged victim went on to threaten legal action against the former minister.
The out-of-court financial agreement did not include an admission of wrongdoing by the ex-minister, it is understood.
A second official, who had worked with the former minister, told The Independent they were aware of the allegations and had also been subject to inappropriate remarks.
She said “it was important that people understand that this isn’t a one-off” in terms of his alleged behaviour.
No 10 declined to comment last night, saying the matter relates to Ms Truss’ leadership bid. Spokespeople for Ms Truss did not respond to a request for comment.
Concerns about inappropriate behaviour swirled around Westminster during Mr Johnson’s premiership amid fears it was going unchecked.
The handling of allegations involving MP Chris Pincher, the former minister accused of groping young men at a private members club, was the final straw in the former PM’s protracted downfall.
Rejecting calls for an ethics adviser, Ms Truss told a Conservative leadership hustings in August that she would “ensure the correct apparatus is in place so that people are able to whistleblow” – but union bosses fear that, without a figurehead, it will be “difficult” for victims of misconduct, especially civil servants, to seek justice.
Mark Serwotka, general secretary of the Public and Commercial Services Union (PCS), which represents thousands of civil servants, said: “By choosing not to appoint an independent ethics adviser, Liz Truss appears to show the same indifference to ministerial misconduct as her predecessor.”
A spokesperson for the PCS added that there was a “lack of willingness” under Mr Johnson’s administration to investigate allegations of ministerial misconduct, “making it difficult for victims to speak out and ensure disciplinary action was taken”.
Last week, the ICGS dropped a complaint made against Mr Pincher because the incident did not occur on the parliamentary estate. At least one of the alleged victims has lodged an appeal to parliament’s standards commissioner, according to reports.
Sources in a range of roles across Westminster have said that there is often little effective recourse for alleged victims. One said that there was often “a choice between speaking out and pushing for something to be done, or holding onto your career”. Others have warned of a culture of cover-ups when it comes to ministerial misconduct.
The Parliamentary Commissioner for Standards said it “has no authority to investigate complaints about how government ministers carry out their ministerial responsibilities”.
Labour’s Jess Phillips, who has advocated for greater transparency in handling complaints across Whitehall, said there was a “clear gap in the systems for civil servants working with ministers”.