The organisation, which represents more than 500 mosques, schools and associations in Britain, has urged James Cleverly, the Tory deputy chairman, to conduct a full audit to tackle the “more than weekly occurrences of Islamophobia from candidates and representatives of the party”.
Mr Cleverly has launched a code of conduct for MPs and local election candidates, which requires members to “encourage and foster respect and tolerance”.
The letter highlights the lack of action regarding Bob Blackman, the MP for Harrow East, who was accused of endorsing Islamophobia after he posted an anti-Muslim article on Facebook.
The post included a link to a story headlined “Muslim Somali sex gang say raping white British children part of their culture” which was published on the website Hardcore News USA, which often features Islamophobic stories.
Mr Blackman, who also retweeted Tommy Robinson “in error” and invited controversial Hindu nationalist Tapan Ghosh, who praised the ethnic cleansing of the Rohingya in Myanmar, to an event in Parliament, apologised for the post saying he “regretted any upset caused”.
The need for a formal inquiry into Islamophobia in the party was described by former Tory cabinet minister Sayeeda Warsi as being “long overdue”.
“I have raised my concerns about Islamophobic comments and campaigning for more than two years and have done so formally and informally including a letter to the Prime Minister,” Baroness Warsi told The Independent.
“The party has been aware of the issue at the highest level and has failed to take the issue seriously and at times even denied its very existence.
“A formal inquiry is now long overdue and I hope my party send a very clear message by establishing this inquiry that bigotry will not be tolerated in a modern Conservative party.”
In recent months there have been a number of Islamophobia-related incidents within the party and several councillors and prospective candidates have either been suspended or forced to stand down.
On 5 April Mike Payne, a Conservative councillor in Calderdale, was suspended after he shared an article which called Muslims “parasites” who “live off the state and breed like rabbits”.
Mr Payne defended himself, saying: “The article refers to the impact of uncontrolled immigration in France. My family is half-French and this is a specific problem.”
Less than two weeks later Alexander van Terheyden, a council candidate in Hackney, was also suspended after he called Islam a “violent political ideology” comparable to fascism and communism on social media.
In response to allegations of Islamophobia, Mr Van Terheyden said: “I’ve stated Islam is a violent political ideology. Note the word ‘political’ and not religious. Note I do not refer to Muslims, I refer to the political ideology.
“My views have always been public. If you mean the fact that I’m happy to voice my discontent for communism, fascism, Islam and other extreme political ideologies there is no secret to this.”
Three days later a Conservative council candidate in Watford, Darren Harrison, was suspended for allegedly supporting white supremacists.
Mr Harrison apparently attended events held by nationalist anti-Islam group Generation Identity.
He denied being a supporter of the group and said: “I do not support their views, but support their right to have their views, as I do anyone else, as long as it does not promote violence which to my knowledge, it does not.”
On 24 April Phillipa Auton stepped down as the council candidate in Hounslow after she responded to a story about the 2016 Berlin attacks by tweeting: “Revoke Muslim immigration, repatriate and secure European borders, keep Europe safe”.
She stood by her comments and said she “supports free speech”.
“You are limited to the number of characters you use in a tweet. I am against illegal immigration and I support having closed borders,” she said.
The next day the Conservative mayor of Wokingham, Peter Lucey, also stood down after a number of social media posts about Islam and the English Defence League.
Mr Lucey said: “Some past social media posts came to light and those are not appropriate for the town mayor.
“I resigned for that reason, and I fully apologise to everyone involved. I would like to apologise to the people of Wokingham and to my party, and I resign from all of them.”
On 27 April, Nick Sundin, a Tory council candidate in Newcastle, was suspended after he tweeted the Prophet Mohammed was a “f****** paedophile”.
He did not respond directly to allegations of Islamophobia but did delete his Twitter account.
Less than a week later, Karen Sunderland, a council candidate in Lewisham, was suspended after old tweets emerged where she called Islam “the new Nazism”.
After the story emerged Ms Sunderland’s Twitter account was deleted.
On 1 May David Boston, a council candidate in Enfield, posted a picture of bacon hanging on a door handle as a way to “protect your house from terrorism” – he was suspended by the party pending an investigation.
Three weeks later Stephen Goldsack, a Scottish Conservative councillor in North Lanarkshire was expelled from the party after it was uncovered that he had formerly been the “Scottish security adviser” for the BNP.
He allegedly rejected an application for a mosque, saying it would be okay if it was a church.
Harun Khan, secretary general of the Muslim Council of Britain, said the number of examples of alleged Islamophobia within the party was a “serious concern”.
He said: “The Conservative Party prides itself in being against any form of bigotry and racism yet there are serious concerns that its best values are being disfigured by Islamophobic views.
“We look forward to the party taking forward our suggestion of an inquiry into Islamophobia and we are happy to help support in any capacity we can.”
When asked by The Independent if investigations into Islamophobia were still underway and what steps were being taken to tackle the issue, a Conservative Party spokesperson said: “We do not comment on ongoing investigations.”