Boris Johnson met with Nusrat Ghani after she was sacked over "concerns of her Muslimness", Downing Street has claimed.
Number 10 officials say the Prime Minister wrote to Ms Ghani after they had a discussion and he expressed "his serious concern" of the "serious claims".
The PM then wrote to the Tory MP for Wealden more than a week after their meeting, the Mirror understands.
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 said her "Muslimness was raised as an issue" at a Downing Street meeting, she told the Sunday Times.
The whip also 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.
A Number 10 spokesperson has 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 concernHe then wrote to her expressing his serious concernHe then wrote to her expressing his serious concernHe 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."
After she bravely spoke of the alleged incident, Government Chief Whip Mark Spencer took to Twitter to identify himself as the person behind the MP's claims.
In one now-deleted tweet, he wrote: "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."
Deputy Prime Minister Dominic Raab has said there will be no “specific investigation” into her claim.
