Downing Street has said an investigation into allegations of Islamophobia linked to the former chief whip Mark Spencer should not be pre-empted, following his appointment as Commons Leader.

Last month Prime Minister Boris Johnson asked the Cabinet Office to “establish the facts” regarding Tory MP Nusrat Ghani’s claim that she was sacked as a minister because of concerns about her “Muslimness” in 2020.

Ms Ghani said she was told by a Government whip that her faith made colleagues “uncomfortable”.

Mr Spencer confirmed he was the subject of the claims, but strongly denied making the alleged comments, saying the accusations were “completely false” and “defamatory”.

Asked about reported criticism from MPs over Mr Spencer’s move from chief whip to Commons Leader on Tuesday, given the ongoing investigation into the allegations, the PM’s official spokesman said conclusions should not be drawn pre-emptively.

“As you say, there is an investigation ongoing to establish the facts of what happened. And that’s being carried out in a process… in line with a due process,” he said.

“It’s right that we need to allow that investigation to conclude without… pre-empting it or drawing conclusions whilst that work is ongoing.”

The Cabinet Office probe was ordered by the PM in January after Ms Ghani claimed to The Sunday Times that she was demoted from the position of transport minister in 2020 due to her Muslim faith.

The MP for Wealden in East Sussex said a Government whip told her that her “Muslimness” had been raised as an issue.

Mr Spencer identified himself as the whip in question, but denied the substance of the alleged conversation.

Health Secretary Sajid Javid described both Mr Spencer and Ms Ghani as friends when asked about the investigation by reporters, and said it was “right” that there was a probe into the “serious allegations” that had been made.

Mr Javid, speaking after a hospital visit in east London, said: “The investigation being referred to is being carried out by the Cabinet Office.

“Anyone being investigated would have nothing to do with the investigatory process itself. It is right that there is this investigation.

“These were serious allegations.

“It is also fair to put on the record that Mark, who is a friend and colleague, as well as Nusrat Ghani, who made the allegations and they are both friends and colleagues, that Mark has said that he doesn’t recognise any of those words that have been attributed to him.

“He is a friend and a colleague and I think he will do a very good job in the position he has been given.”