The joint study by the Methodist Church and the Church of England finds work focusing on developing values is often surviving "in spite of rather than being encouraged by" further education funding changes.
To get cash tutors are having to turn informal courses which encourage debate on moral questions into programmes leading to qualifications.
The step has led some to question how they can measure the "outcomes" of programmes whose value may only become real to students in future years as they mature.
Growing tension between outcome-related funding and values teaching was this week described by the Rev Clifford Jenkins, the Churches' national adviser in FE, as "a battle for the soul of further education".
The new study, which stems from research to highlight current practice in values development in FE, echoes the warning issued in last year's annual report by FE chief inspector Terry Melia.
Dr Melia's report endorsed the value of "enrichment activities" such as courses dealing with moral and spiritual development, but added that "there is a concern in the sector that they may become casualties of the efficiency gains driven by the funding mechanism".
Only accredited courses leading to a qualification can earn money for colleges under the funding system laid down by the Further Education Funding Council.
David Paterson, a history tutor at King Edward VI College, Nuneaton, has had to seek accreditation through the Open College Network for his "matters of life and death" course, devised before incorporation. Students taking the optional programme, which centres on discussing a range of moral issues, are now assessed on progress at the year's end to secure a certificate, and funding for the college.
Mr Paterson said: "I have had nothing but support from the college, but I feel the funding system militates against this kind of course. The trouble is they want to measure everything, but the benefits of courses like these need to be measured over a lifetime."
The Churches' report also warns that the mechanism could not only sideline general programmes but could also lead to values elements being left out of courses training students to enter the caring professions. It calls on bodies devising such courses to ensure they are included.
The Rev Jenkins said: "The time and money pressures are such that if discussion of values is not included in the curriculum it will disappear. "
He added: "We must ask now who it is that FE actually belongs to? Is it students, staff and the community, or is it to be taken over by the approach and language of commerce and industry?" The study will be seen by the harder-nosed as a failure by Churches to face up to the harsh realities of post-incorporation FE.
Others suggest measures such as the shift to outcome-related funding need not be viewed negatively.
Bernard Smith, general secretary of the Association of Principals of Colleges and chairman of the National Ecumenical Agency in FE said: "The fact that we do now hang a qualification label on these courses gives them the credence they deserve."
The Churches' study reveals for the first time the diversity of such work in FE. Many colleges are trying to instate values development across the curriculum and in policy statements and codes of ethics.
A total of 240 chaplains, traditionally more likely to be found in schools or universities, are now working in the further education sector.