The prime minister reportedly said he "couldn't get involved" after a Muslim MP urged him to instigate an inquiry after claiming to have been sacked due to her "Muslimness", she said.
Conservative MP Nusrat Ghani says Boris Johnson told her he couldn't involve himself in the row after she was fired as a junior transport minister in the re-shuffle of February 2020.
Ms Ghani alleges that after the re-shuffle a Tory whip said her belief in Islam "raised an issue"..
The PM wrote to Ms Ghani "expressing his serious concern" and "invited" her to complain formally, according to the Number 10 spokesman.
But Ms Ghani has now released a statement, and says Mr Johnson refused to get involved after she "urged him to take it seriously" and "instigate an inquiry".
The statement, reported by Sky News, says: "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."
The Mirror understands that the PM initially wrote to the Tory MP for Wealden more than a week after their meeting.
Ms Ghani was a transport minister from January 2018 until February 2020.
The married mum became the first female MP to hold her seat in 2015, winning with a majority of 22,967.
She considered quitting politics after her interaction with a Government whip who reportedly said her "Muslimness was raised as an issue" at a Downing Street meeting, she told the Sunday Times.
The whip is also claimed to have said her "Muslim woman minister status was making colleagues feel uncomfortable", and questioned her loyalty to the Party.
The meeting in question was held back in March 2020, reports say.
In the full Number 10 statement, the spokesman said: "After being made aware of these extremely serious claims, the Prime Minister met with Nusrat Ghani to discuss them.
"He then wrote to her expressing his serious concern and He then wrote to her expressing his serious concern.
"She did not subsequently do so. The Conservative Party does not tolerate prejudice or discrimination of any kind."
