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Louise Casey, a senior civil servant, said her study exposed "uncomfortable truths" about the impact of large-scale immigration, in particular discrimination against women in some South Asian communities.
"Inequality within certain communities in these highly segregated areas is getting worse, not better," she told the BBC.
She admitted her findings would put further pressure on Britain's 2.8 million Muslims, amid concerns about rising Islamophobia.
But in a foreword to the report, she warned: "A failure to talk about all this only leaves the ground open for the far-right on one side and Islamist extremists on the other.
"Every person, in every community, in every part of Britain, should feel a part of our nation and have every opportunity to succeed in it. There can be no exceptions to that by gender, colour or creed."
Government officials had reportedly sought to water-down the study, which was commissioned by former prime minister David Cameron last year, because of its controversial findings.
Casey said that people of Pakistani and Bangladeshi origin were more likely to live in residentially segregated communities than other ethnic minority groups, pointing to areas where up to 85 percent of residents were Muslim.
She warned that many people in those areas did not have the same opportunities as others across Britain, often because they did not speak English, and also because cultural and religious practices held them back.
This was particularly true of women, and Casey warned that domestic abuse, female genital mutilation and forced marriage remained "all too prevalent" in some communities.
"It is the misogyny and the patriarchy that has to come to an end. Leaders that are not Muslim and are Muslim need to unite around unity in this country," she told the BBC.
Communities minister Sajid Javid said the report was a "valuable contribution".
"We need to take a serious look at the facts and must not shy away from the challenges we face," he said.
But Mohammed Shafiq, chief executive of the Ramadhan Foundation, a Muslim lobby group, condemned it as "inflammatory and divisive".
"Sadly in today's Britain, Muslims are seen as an easy target to attack by politicians, commentators and parts of the media without any regard for the impact this has on communities," he said.
"There was no mention about the responsibility of the white community to help with integration, as many white families flee mixed areas as ethnic minorities move into a particular area."
He also noted that the government had cut funding for English language classes -- one of Casey's recommendations to improve integration.
The report also said immigrants should take an oath of integration with British values and society on arrival in the country, rather than waiting until their final citizenship test.
Casey urged the promotion of British laws, history and values within the core school curriculum to build "integration, tolerance, citizenship and resilience".
She also called for greater mixing among young people through activities such as sport, and efforts to raise employment levels among marginalised groups.