More than 230 schools have applied to councils for exemption from the legal requirement to hold a daily act of collective worship of a "wholly or mainly of a broadly Christian character".
In some of these schools, Islamic assemblies are held instead, with readings from the Koran. Other schools run secular or multi-faith assemblies where Christianity is avoided or relegated to just one example of a faith among many.
Religious organisations said Christianity in schools was being marginalised and accused schools of failing children.
"The worst thing of all that schools can do, whether they have a determination or not, is a multi-faith mish mash," said Colin Hart, the director of the Christian Institute.
"The British Social Attitudes survey found that 69 per cent of parents backed daily prayers in schools. Yet Christianity in schools is being marginalised. Parents do not want assemblies to be either secular or a confusing amalgam of faiths. Look at the massive number of parents of other faiths who apply to Church schools. They don't like the secularism that is pervading community schools."
The scale of the opt-out can be revealed for the first time after 105 councils in England responded to a Freedom of Information request from The Sunday Telegraph.
Between them, the local authorities had granted "determinations" to 185 primaries and 45 secondaries, teaching an estimated 96,000 pupils.
In most schools with opt-outs, the vast majority of pupils were from ethnic minorities. However, in some, white British pupils formed a sizeable minority.
Inner city authorities, such as Birmingham, Bradford, Leicester and the London boroughs of Brent, Hounslow and Ealing, had dozens of schools which had dropped Christian assemblies. Government figures show that the number of ethnic minority pupils in English schools is growing. One in four primary schoolchildren is from an ethnic minority – double the figure a decade ago.
A number of councils with high numbers of ethnic minority pupils, such as Tower Hamlets and Hackney, in London, had no exemptions. But religious experts said this did not necessarily mean that Christian worship was taking place.
The Church of England said the law was flexible enough to cater for mixed school intakes, without the need for opt-outs.
"Collective worship within a broadly Christian framework rarely poses an issue for students of other faith backgrounds, which tend to share the same core values," said a spokesman.
"The law is sufficient flexibility for schools to be able to reflect the nature of a multicultural intake without needing a determination. For instance, almost half of the content could be from a non-Christian faith. If parents are uncomfortable with what is on offer, they have the legal right to withdraw their child from what is provided by the school."
The duty on schools to provide a daily act of Christian worship dates back to 1944 but was strengthened in the 1988 education act.
Schools can apply to the local authority Standing Advisory Council for Religious Education (SACRE), made up of school and faith representatives, for an exemption from the "broadly Christian" requirement for some or all of their pupils. If this "determination" is granted, the school must provide alternative worship for these pupils.
In 2007, sixth forms were given the right to opt-out of collective worship and in 2008, a committee of MPs recommended that under-16s should also be given the choice.
Many head teachers and their staff object to the requirement and bend or break the rules, particularly in secondary schools. Ofsed is supposed to check that schools do comply but some critics said inspectors took too broad a view. In 2004, David Bell, the then chief inspector and now the permanent secretary of the Department of Children, Schools and Families, suggested that the law on Christian worship be repealed.
John Dunford, the general secretary of the Association of School and College leaders, said: "The concept of compulsory worship has always been a nonsense. Schools have long wanted the government to take on the bishops in the House of Lords and change the law. School assemblies are a valuable way to reinforce the ethos of the school. They often contain the spiritual element that is missing in many children's lives but having a law which imposes Christian collective worship is nonsense."
Terry Sanderson, the president of the National Secular Society, said: "Requiring children to worship, as our law does, is a breach of their human rights. In many schools, children from other creeds and none are in the majority and the proportion is rising. Enforced Christian Collective worship has therefore gone beyond being an embarrassment to becoming a needless source of conflict."
Bordesley Green Girls' Specialist and Enterprise School, in Birmingham, was granted a determination in 2004 which allows it to hold a daily act of worship which is Islamic in character.
Nearly all the pupils at the smaller than average secondary are from minority ethnic groups, the vast majority are Muslim.
Girls at the school, rated "outstanding" by Ofsted, receive a five minute broadcast each morning from the public address system in the head teacher's office. The broadcasts include readings from the Koran and presentations on moral, religious and ethical issues from the pupils themselves. The scripts are agreed in advance by the head teacher. In one broadcast for instance, girls discussed bullying: "Please Allah, we should not bully as this is not following the prophet's way of life," said one.
Clare Considine, the head teacher, said: "We have a system in school which works really well and which has the full support of parents."
Taylor Road School, in Leicester, has not applied for an opt-out from Christian worship, despite an intake which is 85 per cent Muslim. About 5 per cent of the 550 pupils are Christians.
Collective worship involves a theme that runs through the week, based on the moral and spiritual precepts that underpin Christianity and other major religions, such as helping your neighbour, telling the truth and forgiveness.
Chris Hassall, the head teacher, said: "All these themes can be described as "broadly Christian" and we do mention God, as children from all the major religions believe in God. We don't sing hymns or religious songs or read from specific religious texts. A teacher might read out an inspirational or moral story or fable and children are given a chance to reflect on what they have heard."
The school also celebrates major religious festivals in its collective worship, such as Christmas, Easter, Diwali and Eid-ul-Adha. Some parents withdraw their children from these sessions.
Mr Hassall said: "We have not requested a determination because we have interpreted the phrase "broadly Christian" to cover what I've described. A bishop might not think that it adheres to the letter of the 1988 law but you have to be pragmatic.
"Schools should be reflective of society and the community they serve but also need to bear in mind the needs of minorities. Sometimes, if you adopt a blanket approach, that may fit in with the majority but you are not taking account of the minority. We could ask for a determination and concentrate more on Islam but what about the two Christians in the class, for instance."
Priestmead Middle School, in Harrow, Middlesex, consulted parents about how best to provide broadly Christian assemblies yet remain sensitive to the school's multi-faith intake. The majority of pupils are of Asian origin but a total of 20 ethnic groups are represented at the school.
Parents who responded accepted that most of the assemblies would have some sort of Christian bias and said they wanted their children to learn about Christianity and the Bible as this was the culture of Britain. One Muslim parent commented that the content of the assemblies, held at the end of the school day, helped her children see the links between Islam and Christianity.
The collective worship policy that emerged ensures that children appreciate different approaches to faith. The words "Lord" or "God" are sometimes used to acknowledge a deity. A record of topics covered in collective worship is kept to ensure the majority are "broadly Christian".
Alison Stowe, a teacher at the school and chair of Harrow SACRE, said: "This week for instance we covered the story of the three wise men. We read a bit from the Bible, then we discussed how the wise men could have been Zoroastrians and we looked at the Farsi bible version."
Shaw Hill Primary School, in Birmingham, runs one Islamic assembly and four multi-faith assemblies each week. The school, where the vast majority of the pupils are of Pakistani background, was granted a "part" determination in 2003 which allows it to offer alternative collective worship to a group of pupils.
Margaret Barnfield, the head teacher said: "The school had a greater mix of pupils when we originally applied for the Determination, hence the multi-faith element but we feel that all the children, whatever their heritage, benefit from a broad outlook on all the faiths."