A cabinet minister promoted by Boris Johnson despite allegations of Islamophobie has revealed that an investigation into him is being conducted by the prime minister’s personal ethics adviser.

Mr Johnson initially said the probe into close ally Mark Spencer would be carried out by Cabinet Office civil servants. The involvement of Lord Geidt suggests it has been escalated.

He today said he found it “rough” that he was unable to defend himself against the accusations from Tory MP Nus Ghani in public until the inquiry is over – even though it was Mr Spencer himself who first revealed he was the subject of her complaint.

The news came as a union representing Westminster staff voiced “concern” at Mr Spencer’s appointment on Tuesday as Leader of the Commons while he remains under investigation.

Garry Graham, deputy general secretary of Prospect, warned the appointment could hit staff confidence in the Leader’s office unless the probe is completed swiftly.

“Prospect notes with concern that the new Leader of the House of Commons, who has responsibility for standards in the House, is himself under investigation,” said Mr Graham.

“We trust that this investigation will be concluded thoroughly and promptly so that staff in the House can maintain confidence in the system and in the Leader of the House.”

The inquiry into Mr Spencer stems from Ms Ghani’s claim last month that she was told in 2020 she was being moved from a government post because her “Muslimness” made others uncomfortable.

Mr Spencer, who was then chief whip, outed himself as the other person in the conversation and referred himself for investigation. But he rejects Ms Ghani’s account of his comments and insists he said nothing Islamophobic. Ms Ghani was the first female Muslim minister at the time of her initial appointment.

The Sherwood MP told BBC Radio Nottingham today: “That investigation is ongoing… we wait for the results of that.

“That is a bit rough, when you’re accused of something of that nature. It’s a bit rough not being able to defend yourself until the results of that investigation come forward.

“I’ve just got to keep my mouth shut, present the facts to Lord Geidt – who’s doing the investigation – and then once that’s concluded, I think we’ll be able to have a fairly open conversation about that.”

Mr Johnson asked the Cabinet Office to “establish the facts” last month, but there has been no announcement of the probe being handed over to Lord Geidt. A spokesperson for the PM confirmed that Ms Ghani spoke to him about her concerns in 2020 and was encouraged to use the Conservative Party’s internal complaints process.

Health minister Ed Argar today said Mark Spencer had been a “highly effective” chief whip, and that it would not be right to comment on the ongoing investigation.

Asked about Mr Spencer’s move during Tuesday’s mini-reshuffle, Mr Argar told Times Radio: “Speaking on the basis of my working relationships, and as a colleague, I’ve always found Mark to be an incredibly decent, forthright and genuine person and I found him to be a highly effective chief whip.

“And from my perspective as a minister taking legislation through the House of Commons… indeed at the moment, I rate Mark’s skills very highly and I look forward to working with him as Leader of the House in helping to get my legislation through, as well as every other piece of legislation.”