The study, for the Arts and Humanities Research Council, also claims that there is no clear guidance for parents, who are often unaware they can opt out their children from religious assemblies if they so wish.
All British schools are obliged by law to offer acts of collective worship, which must be Christian in nature unless the school is a non-Christian faith school.
The report, conducted by the University of Leicester, said: "Where the aims for the duty of collective worship are set out, these appear contradictory in the context of a diverse pupil population, specifically the aims to provide an opportunity to worship God yet simultaneously to develop a community spirit and promote a common ethos."
The statutory duty to provide an act of collective worship/religious observance in schools was introduced in 1945.
It is feared many parents have not been told that they can choose for their child to be exempt.
The paper recommends that all educational authorities in the UK issue guidelines to schools to clarify that the right to withdraw from acts of collective worship extends to all schools.
All schools should also clearly publicise the content and format of acts of collective worship or religious observance, so that parents and pupils are knowledgeable about what happens during these activities, and able to make informed decisions about whether to opt out.
Keith Porteous Wood, Executive Director of the National Secular Society, told Premier that there are other rules few people know about: "Sixth form pupils can withdraw themselves from collective worship. That is a reform that the National Secular Society arranged through Parliament a few years ago."
"I do not think it is appropriate to have collective worship in community schools because society generally is not religious and there are a lot of people from other faiths."
Mr Porteous Wood also believes pupils are having worship imposed upon them by the state.
He said: "I think it is absolutely appalling that the law as it stands requires schools to provide a daily act of worship.
"The act says 'shall take part in' not 'shall attend'. If we ever took a case on that I think it would probably be in breach of the human rights of the children."
Premier contacted groups that have expressed support for a Christian element of school worship, but none were available for comment.
The report also highlights how in 2004, the Chief Inspector of Schools for England drew Parliament's attention to the fact that 76% of secondary schools were breaking the law by failing to provide daily acts of worship.
A Department for Education spokeswoman said: "Collective worship plays an important role in schools. It encourages children to reflect on belief, and the role it plays shaping fundamental British values of tolerance, respect and understanding for others.
"It is for schools to tailor their provision to suit the needs of their pupils, and parents can withdraw their children from all or any part of collective worship."