Lee Anderson has been suspended from the Conservative Party after claiming that Sadiq Khan is controlled by “Islamists”.
The decision came after the ex-Tory deputy chairman refused to apologise for his controversial remarks.
Pressure had been mounting on Rishi Sunak to take action over the comments from the Ashfield MP.
Mr Khan said the “deafening silence” of the Prime Minister and his Cabinet on the matter amounted to condoning racism.
A spokesperson for Chief Whip Simon Hart said: “Following his refusal to apologise for comments made yesterday, the Chief Whip has suspended the Conservative whip from Lee Anderson MP.”
It comes after Mr Khan accused Mr Anderson of “pouring fuel on the fire of anti-Muslim hatred” after he said Islamists had “got control” of him.
He said the comments were Islamophobic and send the message that Muslims are “fair game” when it comes to racism.
On GB News, Anderson said of Mr Khan, the first Muslim to hold the role: “He's given our capital city away to his mates. I don't actually believe that the Islamists have got control of our country, but what I do believe is they've got control of Khan, and they've got control of London.”
A Conservative source was defending Mr Anderson as recently as Friday evening before he was stripped of party support on Saturday.
Cabinet minister Grant Shapps distanced himself from the remarks on Saturday morning but stopped short of condemning his fellow MP, arguing that people should be allowed to “speak their mind”.
However, business minister Nus Ghani and senior backbencher Sir Sajid Javid were among other senior Tory figures joining a growing chorus of criticism from across the political divide.