Earlier, the prime minister's official spokesman confirmed the pair met to discuss her claims that a Tory whip told her her faith was "raised as an issue" after she was sacked as a junior transport minister in a February 2020 re-shuffle.

The spokesman added that nine days after the conversation, Mr Johnson "wrote to her expressing his serious concern" and "invited" her to lodge a formal complaint.

However, in a statement, Ms Ghani said: "When I told the PM 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.

"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.

"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."

Chief Whip Mark Spencer revealed on Saturday he is the whip Ms Ghani has made the claims about but denied all accusations.

Whip said being Muslim makes MPs 'feel uncomfortable', MP claims

Ms Ghani, MP for Wealden in East Sussex, said the whip told her "Muslim woman minister status was making colleagues feel uncomfortable" and it made her consider quitting as an MP.

She added that they told her there were concerns "that I wasn't loyal to the party as I didn't do enough to defend the party against Islamophobia allegations".

And she said she was warned if she kept raising the claims, her career and reputation would be "destroyed".

Ms Ghani's accusation comes as the tactic of whips is called into question following allegations by some Conservative MPs they have been blackmailed for failing to toe the party line, or even considering it.

The job of whips is to make sure MPs vote on parliamentary business and vote in the way their party wants.

Mark Spencer says he is whip in question

Chief Whip Mark Spencer, revealing he is the whip in question, said the accusations are "completely false".

In Mr Spencer's statement, he 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 this evening.

"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 to be included in the report."

Tory MP: 'Not apparent she was a Muslim so it's a lame excuse'

Conservative MP Michael Fabricant, who has been defending Mr Johnson recently, said he did not buy Ms Ghani's "excuse" as she is not "obviously a Muslim".

"I think the whole thing actually stinks, the accusation made by Nus Ghani," he told LBC.

"For her to say that someone had said it's because she's a Muslim - I mean she's hardly someone who's obviously a Muslim. I had no idea what religion she is.

"The Labour MP Keith Vaz, who was of South Asian origin, he actually I do know because we discussed it, he's no longer an MP, but he's a Goan Christian and others are Hindus and others are Muslims and whatever.

"But with her, it wasn't apparent so it does seem rather a lame excuse to me."

Ms Ghani could still make formal complaint

Deputy PM Dominic Raab said Ms Ghani could still make a formal complaint, which would allow for an investigation into the matter.

He told Sky News' Trevor Phillips on Sunday: "It is incredibly serious, let me be clear at the outset, we have absolutely zero tolerance for any discrimination, any Islamophobia in the Conservative Party."

Mr Raab added it was "very unusual" Mr Spencer has revealed he is the person accused but said he "categorically denied" it.

Health Secretary Sajid Javid said Ms Ghani is a friend and her claims are "very serious" and need a "proper investigation".

"I would strongly support her in making a formal complaint - she must be heard," he added.

'Like being punched in the stomach'

Ms Ghani told The Sunday Times her experience was "like being punched in the stomach. I felt humiliated and powerless".

She said she was later warned that continuing to raise the issue would leave her "ostracised by colleagues" with her career and reputation "destroyed".

"When I challenged whether this was in any way acceptable and made clear there was little I could do about my identity, I had to listen to a monologue on how hard it was to define when people are being racist and that the party doesn't have a problem and I needed to do more to defend it," she said.

"It was very clear to me that the whips and No 10 were holding me to a higher threshold of loyalty than others because of my background and faith."