The segregation was discovered by Britain's schools inspectorate during a visit to Darul Uloom Islamic high school in Birmingham.
"During the inspection of Darul Uloom Islamic high school [in Birmingham], the actions of governors did not model the promotion of mutual respect for men and women," Michael Wilshaw, chief inspector of Ofsted - which is reviewing the standards at Britain's Christian and Muslim faith schools - wrote to UK education minister Nicky Morgan this week.
Ofsted found another school's library contained literature with extremist and sexist views.
The inspectors of Ofsted had revisited 22 schools previously inspected by Bridge Schools Inspectorate(BSI), an agency which was abolished two months ago.
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While one was rated outstanding and four were deemed good, eight required improvement and nine were found to be inadequate.
Michael said the findings were seriously concerning, and urged the re-inspection of all schools previously monitored by the BSI, as a priority.
"All schools must promote the fundamental British values of democracy, the rule of law, individual liberty, and mutual respect for different faiths and beliefs," said a spokesperson of UK Department for Education.
The investigations follow the "Trojan Horse" scandal which broke out earlier this year over fears of extremist groups taking over the agenda at schools in Birmingham.