Conservative MPs’ support for Boris Johnson over his comments comparing Muslim women in burkas to bank robbers has “shone a light on the underbelly of Islamophobia” within the party, the Muslim Council of Britain (MCB) has said.

Harun Khan, MCB secretary general, said the former foreign secretary’s comments, which have attracted criticism and divided opinion since appearing in the Daily Telegraph on Monday, had a “real and worrying” impact on the Muslim community.

He also said the MCB received Islamophobic hate mail off the back of the furore, some describing Muslims as “barbarians”.

Mr Khan’s comments came as fellow prominent Conservative Jacob Rees-Mogg said the party’s investigation into Mr Johnson had been set up as a “show trial” in a bid to derail any plans the former Cabinet minister may have to seek the Tory party leadership.

Mr Johnson is yet to respond to the furore sparked by the article, in which he opposed a ban on the burka or niqab, but branded the face-covering veils “ridiculous” and “oppressive” and said Muslim women wearing them looked like letter-boxes or bank robbers.

He made no comment to waiting reporters as he returned home from a holiday abroad on Saturday, but is expected to break his silence in his next Telegraph column on Monday.

In a statement, Mr Khan said: “The impact of Boris Johnson’s comments are real and worrying and indicate the importance of a full, transparent and independent investigation into his conduct, in particular given the lack of action in previous cases of Islamophobia in the party.

“The comments and belief by a number of Conservative MPs that not even an apology is required has shone a light on the underbelly of Islamophobia that is present within the party – one that can only be tackled by sincerely changing course and positively responding to calls for an independent inquiry into Islamophobia in the party.”

Further condemnation came from Andrew Cooper, David Cameron’s former Downing Street aide, who pulled no punches with his assessment of Mr Johnson.

In a Twitter post, he wrote: “The rottenness of Boris Johnson goes deeper even than his casual racism and his equally casual courting of fascism.

“He will advocate literally anything to play to the crowd of the moment. His career is a saga of moral emptiness and lies; pathetic, weak and needy; the opposite of strong.”

There were further signs of grassroots Tory anger over the affair, with the Telegraph giving over its whole letters page to reaction from readers after being “inundated” with messages of support for Mr Johnson.

And it was reported that letters have been sent to the party complaining about chairman Brandon Lewis, whose demand for an apology from Mr Johnson provoked an escalation in the row earlier this week.

Mr Rees-Mogg suggested the attacks on Mr Johnson’s comment were a reflection of “envy” felt towards him because of “his many successes, popularity with voters and charisma”.

The howls of outrage directed at the former figurehead of the Leave campaign were “suspect” and the motivations of those attacking him “dubious”, said the North East Somerset MP.

“Could it be that there is a nervousness that a once and probably future leadership contender is becoming too popular and needs to be stopped?” asked Mr Rees-Mogg.

“This may explain the attempt to use the Conservative Party’s disciplinary procedures, but it has been handled so ham-fistedly that it brings only sympathy and support for Mr Johnson.”

And he added: “When Margaret Thatcher was leader, she and Michael Heseltine were hardly soulmates, but she would not have allowed personal rivalry to take the heat off the Labour Party, whose own deep internal divisions are buried in other news now, nor would she have countenanced any attempt to have a show trial.

“Attacking Boris merely helps the Opposition. It is time for good sense to assert itself, free speech to be encouraged and, as the summer rain falls, for hot-headed action to be cooled down.”

Mr Johnson’s comments on the burka have been branded “inflammatory and divisive” by the Equality and Human Rights Commission, but the watchdog made clear it was not launching its own investigation.

A panel including one independent figure, one representative of the voluntary party and one nominated by the backbench 1922 Committee, will look into complaints that Mr Johnson’s comments breached the Conservative Party’s code of conduct.

Under party rules, the head of the panel may dismiss the complaints if they are found to be obviously trivial, lacking in merit or unable to be fairly investigated.

Disciplinary action could lead to Mr Johnson being suspended or even expelled from the Tories, but would risk igniting civil war in a party many of whose members see him as the best option to succeed Mrs May as leader.

But there have also been suggestions that he could be ordered to attend a diversity training course.