“The prime minister has now asked officials to establish the facts about what happened,” a No 10 spokesperson said.
Mr Johnson was under fierce pressure to act after telling Ms Ghani – nearly two years ago – to start a formal complaint with the party about the way she was treated.
The former junior transport minister said she had told him this was “very clearly not appropriate for something that happened on government business”.
Ms Ghani alleged that, when she was sacked in 2020, Tory whips told her that her “Muslim woman minister status was making colleagues feel uncomfortable”.
She told The Sunday Times: “It was like being punched in the stomach. I felt humiliated and powerless.”
The Tory chief whip, Mark Spencer, has identified himself as the person accused of making the remarks, but said: “These accusations are completely false and I consider them to be defamatory. I have never used those words attributed to me.”
After 24 hours of delay, A No10 spokesperson said: “The prime minister has asked the Cabinet Office to conduct an inquiry into the allegations made by Nusrat Ghani MP.
“At the time these allegations were first made, the prime minister recommended to her that she make a formal complain to CCHQ [Conservative Campaign Headquarters]. She did not take up this offer.
“The prime minister has now asked officials to establish the facts about what happened. As he said at the time, the prime minister takes these claims very seriously.”
Ms Ghani welcomed the announcement, but said she needed to see the terms of reference for it.
“The terms of reference of the inquiry must include all that was said in Downing Street and by the whip,” the Conservative backbencher argued.
It is understood that Mr Johnson spoke with Ms Ghani on Sunday evening to inform her that that he had ordered the inquiry.
The move comes eight months after the Conservatives apologised to victims of Islamophobia and racism in the party, after an inquiry.
It promised to act after Professor Swaran Singh’s report branded the Tories’ complaint-handling unfit for purpose and warned “anti-Muslim sentiment remains a problem”.
An action plan followed, but some critics branded the inquiry “a whitewash” and called for the equalities watchdog to launch its own investigation.
Sayeeda Warsi, a former Conservative chair, said the Singh report had exposed “a system that failed to protect victims of racism”, who were “painted as troublemakers for speaking out”.
She welcomed the new inquiry, but condemned the “pattern in these cases” that her party fails to take Islamophobia “ as seriously as other forms of bigotry”.
“That creates a fear in others not to raise this issue. There is never a proactive response. Action is rarely taken until the media is involved,” she said.
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