The 49-year-old MP lost her job as transport minister in February 2020 as part of a mini-cabinet reshuffle.
Ms Ghani alleged in an interview with The Sunday Times she was told by a whip her ‘Muslimness was raised as an issue’ at a post-reshuffle meeting and her status as a Muslim woman and a minister was ‘making colleagues feel uncomfortable’.
Following the allegations, Chief Whip Mark Spencer took to Twitter to identify himself as the person Ms Ghani’s allegations were about.
The MP for Sherwood said: “To ensure other Whips are not drawn into this matter, I am identifying myself as the person Nusrat Ghani MP has made claims about.
“These accusations are completely false and I consider them to be defamatory. I have never used those words attributed to me.
“It is disappointing that when this issue was raised before Ms Ghani declined to refer the matter to the Conservative Party for a formal investigation.
“I provided evidence to the Singh Investigation into Islamophobia which concluded that there was no credible basis for the claims be included in the report.
“These claims relate to a meeting in March 2020. When Ms Ghani raised them she was invited to use the formal CCHQ complaints procedure. She declined to do so.”
Ms Ghani also told The Sunday Times that she was later warned that continuing to raise the issue would leave her ‘ostracised by colleagues’ with her career and reputation ‘destroyed’.
Speaking on Sky News’ Trevor Phillips on Sunday, Deputy PM Dominic Raab, said Ms Ghani’s claims were ‘incredibly serious’.
He added: “We have absolutely zero tolerance for any discrimination, any Islamophobia in the Conservative Party.”
Mr Raab also said the Wealden MP could still make a formal complaint.
Ms Ghani put out a statement via Twitter this afternoon.
She said: “When I told the Prime Minister in June 2020 what had been said to me I urged him to take it seriously as a Government matter and instigate an inquiry.
“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.
“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.
“Now is not the time I would have chosen for this to come out and I have pursued every avenue and process I thought available to me, but many people have known what happened.
“In my statement yesterday I was careful not to mention any names or implicate the Prime Minister.
“All I have ever wanted was for his Government to take this seriously, investigate properly and ensure no other colleague has to endure this.
“I have many things that I want to achieve in politics, not least my campaigns on human rights and genocide and I am deeply disappointed that it has come to this.”