Thousands of skeletons dug out of British soil could find permanent rest in redundant churches, according to new guidelines drawn up by English Heritage and the Church of England.

A report published at the end of January aims to clear up the confusion surrounding British remains stored in museums.

Archaeologists and curators have long expressed concerns about the best way to treat human remains and have argued that the Home Office licensing system, which is required to dig up human remains, gives insufficient guidance.

Hedley Swain, the head of the early department at the Museum of London which holds 17,000 skeletons, said: 'The licensing system leaves it up to us to decide what is of value, and why... It says that bones should either be reburied or go into archival storage, but it doesn't suggest a time frame for making decisions.'

The new report gives advice to archaeologists and museums about graveyards, suspected burial sites, archaeological sites and redevelopments, and holdings in storage.

It advises minimising disturbances to burials and treating remains with respect, but acknowledges the scientific value of remains and the need to conduct research on them.

The Church of England's position is stated as: 'Following burial, remains should stay in that place of rest, being treated with respect and reverence, although ultimately it is not the physical remains that matter.'

Joseph Elders, the archaeology officer in the cathedrals and church buildings division of the Church of England, said that pressure to issue guidelines on the situation had come from museums and archaeologists, rather than the clergy or public.

Any reburials are accompanied by an ecumenical service reflecting the fact that the beliefs of the deceased are not necessarily known.

The Museums Association has been closely involved in producing the guidelines with Maurice Davies, the MA deputy director, sitting on the steering group. Caitlin Griffiths, the MA's ethics coordinator, said: 'I would have liked to see more guidance on making decisions on what to retain and reburial, but this is still a big step forward: the guidelines provide a lot of practical advice.'

The Museum of London operates a strict policy of dividing collections. Skeletons that are 'disarticulated and destratified', so of no real scientific value, are reburied.

The rest of the collections are either deemed of obvious scientific importance or may have a scientific use in the future that is not immediately apparent.

English Heritage, the Home Office and the Anglican Church are now establishing a permanent advisory group to help museums and archaeologist.