A former Tory minister who claims she lost her job because of her Muslim faith has been urged to submit a formal complaint.

Dominic Raab, the deputy prime minister, said that while Nusrat Ghani’s allegations were “incredibly serious” the party could not investigate them because she had not entered a formal complaint.

Ghani, the Conservative MP for Wealden and transport minister until a Cabinet reshuffle in early 2020, claims she had a conversation with a whip in which they said her “Muslimness was raised as an issue” and that her “Muslim woman minister status was making colleagues feel uncomfortable”.

In an unusual move, chief whip Mark Spencer identified himself on Twitter as the colleague in question and said the accusations were “completely false” and “defamatory”.

A No.10 spokesman said on Sunday that Boris Johnson met with Ghani to discuss her “extremely serious claims” and that he invited her to make a formal complaint, but she did not do so.

“The Conservative Party does not tolerate prejudice or discrimination of any kind,” the spokesman added.

In response, Ghani hit back, claiming Johnson told her he could not get involved, instead referring her to the Conservative party complaints process.

“When I told the prime minister in June 2020 what had been said to me in the government Whips’ office I urged him to take it seriously as a government matter and instigate an inquiry,” she said.

“He wrote to me that he could not get involved and suggested I use the internal Conservative Party complaint process.

“This, as I had already pointed out, was very clearly not appropriate for something that happened on government business – I do not even know if the words that were conveyed to me about what was said in reshuffle meetings at Downing Street were by members of the Conservative Party.”

She added: “Not a day has gone by without thinking about what I was told and wondering why I was in politics, while hoping for the government to take this seriously.

“Those that have not had their identity and faith questioned cannot fully appreciate what it does to you.”

A number of Ghani’s colleagues have rallied behind her since the allegations emerged.

Education secretary Nadhim Zahawi said Ghani was a “friend, a colleague and a brilliant parliamentarian” and that her claims had to be “investigated properly and racism routed out”. Caroline Noakes, chair of the women and equalities select committee, said she was “absolutely appalled”.

Asked by Sky News’ Trevor Phillips whether he believed Spencer of Ghani, Raab said: “I think if there’s any claim like this, a formal complaint should be made and as the chief whip has said, Nus was invited to make a formal complaint, she still is able to do so, and she hasn’t yet done so.

“So I’m not going to start getting into impugning anyone’s integrity.”

On the BBC’ Sunday Morning programme, Raab was asked why Ghani would “make up” the accusations.

“I can’t answer that, all I’m trying to give you a very clear account of what the chief whip said in response…I would say if Nus wishes to do so, she should make a formal complaint so it can be properly investigated.”

In her interview with the Sunday Times, Ghani described the impact the alleged interaction had had on her.

“It was like being punched in the stomach,” she said. “I felt humiliated and powerless.”

Ghani went on to say that she was warned that if she continued to raise the matter she would be “ostracised by colleagues” and her “career and reputation would be destroyed”.

“The feeling of isolation and powerlessness after this episode would not leave me, and I raised it several more times through official party channels and with some colleagues,” she told the newspaper.

“However, after the threats from whips, I was extremely careful to follow procedure, and when the procedure ran out of road I had no choice but to get on with my career and make a difference for my constituents and for the issues I care about from the back benches.”

Ghani’s claims are likely to lead to a further deterioration of relations between some backbenchers and the government following a dramatic week in which the whips were accused of using threatening and intimidating behaviour against MPs who were minded to vote against the government.

Christian Wakeford, the MP for Bury South who defected from the Tories to Labour, claimed he was threatened with having a new secondary school blocked in his constituency if he voted against the government on an issue.

He has since said former chief whip Gavin Williamson was behind the threat.

In response, Williamson has said he does not have “any recollection of the conversation as described but what I do remember is working tirelessly with Christian and others in order to be able to deliver this school, which I did”.

William Wragg, chair of the Public Administration and Constitutional Affairs Committee, is reportedly meeting with the police this week over allegations the whips tried to “blackmail” MPs who have been critical of Johnson’s leadership in the wake of the Downing Street party scandal.

At the beginning of a committee session, Wragg said: “Members of staff at No.10, special advisers, government ministers and others encouraging the publication of stories in the press seeking to embarrass those who they suspect of lacking confidence in the PM is unacceptable.”

Asked about claims earlier this week, Johnson said he had “seen no evidence to support any of those allegations” and Downing Street has said it will not launch an investigation because it had not seen proof.

This week all eyes will be on a report into the alleged Downing Street parties by senior civil servant Sue Gray.

A number of Conservative MPs have indicated they will wait for the outcome of the report before deciding whether to move against Johnson, making its publication a critical moment for his leadership.

In a further blow to the PM, the Sunday Times reported that Gray will also look at allegations that parties were held in his private Downing Street flat.