Sajid Javid said he disagreed with Tory peer Baroness Warsi, who last week backed a call from the Muslim Council of Britain (MCB) for the party to make sure “racists and bigots have no place in the party”.
The MCB wrote to party chairman Brandon Lewis, highlighting a string of incidents by Tory candidates and other representatives ranging from allegedly offensive tweets to accusations of links to the far-right.
Appearing on the Andrew Marr show, Mr Javid hit out at the MCB, saying it did not represent British Muslims and suggested its members had made unacceptable comments about extremism.
He said: “The Muslim Council of Britain does not represent Muslims in this country. You find me a group of Muslims that thinks that they’re represented by the MCB.
“I would be very suspicious of anything that they’ve got to say, not least because under the last Labour government and a policy continued by us, we don’t deal with the MCB and we don’t deal with it because too many of their members have had you know, comments on extremists and that’s not acceptable.”
The MCB’s general secretary, Harun Khan, last week told Mr Lewis that there were “more than weekly occurrences of Islamophobia” by Tory figures in April.
Mr Khan also highlighted the campaign run by Zac Goldsmith in his unsuccessful bid to beat Labour’s Sadiq Khan to become Mayor of London in 2016, saying there had been no action taken against those responsible for “shocking Islamophobia” during the campaign.
On Sunday, Mr Khan said the Home Secretary had “chosen to shoot the messenger”.
He added: “If the response is to instead attack the Muslim Council of Britain, it sadly indicates that the party has no interest in dealing with this matter with the seriousness it deserves.
“We have long spoken out and proactively challenged terrorism and extremism, as have British Muslims across the country.
“The reality of Islamophobia is that Muslims and the Muslim Council of Britain have to deal with the smear of extremism even though they have clearly and consistently condemned violence perpetrated by people who claim to do this in the name of our religion.”