The Churches' Child Protection Advisory Service (CCPAS) surveyed all UK Christian churches and found 6% - about 2,500 - did not have formal policies in place.
David Pearson, the executive director of the CCPAS, being interviewed on the programme, said: 'Government policy says that all churches and all organisations working with children should have procedures in place for responding to situations where children might have been abused and in relation to safe recruitment of staff and practice and so on.
'Churches look after probably more children than any other organisation outside of schools so they should be in the forefront of child protection, particularly since churches are open to everybody.'
The survey had shown that churches were doing extremely well in many areas and were in the forefront of child protection, but Mr Pearson added: 'The worrying thing about this survey is that we discovered that something like 2,500 known churches hadn't introduced any policies at all.
'We just looked at churches. If we'd looked at any other organisation such as schools or others working with children, one might find a similar picture, that there are big gaps in terms of implementing effective policies.'