Inspectors from Ofsted- the Office for Standards in Education - rated 42.5% of private evangelical Christian schools as failing to help pupils learn to respect other cultures and promote "tolerance and harmony", compared to 36% of Muslim schools, the Times Educational Supplement reported on Friday.
Ofsted chief David Bell angered Muslims this week when he said Islamic schools could threaten the coherence of British society.
But the education watchdog defended Bell's comments as a contribution to "important public debates".
Faith school debate
"The number of independent faith schools has grown from 170 in September 2003 to 276 in January 2005," said a spokeswoman. "Independent Muslim schools are now the largest group within this sector and are increasing in number at a faster rate than schools from other faith sectors.
"There are now more than 100 Muslim schools educating more than 14,000 pupils, so these schools educate by far the largest proportion of children being taught in faith schools."
Evangelical Christian schools teach 5000 pupils and Jewish schools cater for 9500 pupils.
"I worry that many young people are being educated in faith-based schools, with little appreciation of their wider responsibilities and obligations to British society"
Head of Ofsted
In a speech to the Hansard Society on Monday, Bell said a traditional Islamic education "does not entirely fit" children for life in modern Britain.
"I worry that many young people are being educated in faith-based schools, with little appreciation of their wider responsibilities and obligations to British society," he said.
The Muslim Council of Britain described Bell's remarks as highly irresponsible while the Association of Muslim Schools accused him of Islamophobia.
However, Ghayasuddin Siddiqui, leader of the Muslim Parliament of Great Britain, urged Islamic schools to take Bell's criticism seriously.
"Muslim schools will be doing a great disservice to their pupils if they do not attend to the criticism made by the chief inspector of schools," Siddiqui said.
"It is time that Muslim schools seriously consider admitting a proportion of children from other faiths to give their Muslim pupils an atmosphere of reality," Siddiqui added.