Inspectors have been asked to survey the ethos of independent faith schools
Ofsted inspectors are to check that schools are promoting tolerance for other cultures, in a survey of independent faith schools in England.
The education watchdog has been asked to examine the spiritual and cultural ethos being taught.
Last month, a think tank claimed some Muslim schools were allowing pupils to be influenced by extremist values.
Schools Secretary Ed Balls said schools must prepare pupils for "life in wider British society".
The Association of Muslim Schools has welcomed the announcement.
"As Muslim schools we believe that we are at the forefront of preparing children and young people to face the challenges of life in modern Britain and to also contribute in a positive way to wider society," said a statement from the association.
'Ethos and values'
The report from think tank Civitas, called Music, Chess and other Sins: Segregation, Integration, and Muslim Schools in Britain, claimed that some Muslim schools were allowing extremist views to be promoted.
The Association of Muslim Schools had attacked that report as "divisive and dishonest".
Mr Balls has now asked Ofsted to carry out a survey in a small number of independent faith schools to investigate how they support the "spiritual, moral, social and cultural development of pupils".
"Some concerns have been raised recently about practice in a small minority of independent faith schools and whether they are effectively preparing pupils for life in wider British society," said Mr Balls.
The survey will consider the "ethos and values" of the schools and the influences on pupils through the curriculum, activities outside lessons and links with other organisations.
A large majority of Muslim schools are within the independent sector - although there are plans for an expansion of Muslim schools within the state sector.
The survey will look at a sample of schools from different faith groups.
In 2005 the then chief inspector of schools, David Bell, sparked a row when he said that independent Muslim schools must make greater efforts to show pupils a "common heritage".