Trainee priests will face a huge rise in university tuition fees if controversial plans to reform university funding go ahead, say senior clerics.

Three quarters of the 1,500 students training to become Church of England clergy at any one time are taking second university degrees because many are coming into the priesthood later in life.

The Church of England is giving warning that plans to remove £100 million for students wishing to take a second degree could have a catastrophic effect on the quality of training for clergy and leave a huge black hole in church finances.

Trainee nurses, teachers and scientists have won exemptions, arguing that they are pursuing strategically important and socially desirable subjects. But the Government has resisted intensive lobbying from the Church to add theology to the list of exemptions.

Instead, Bill Rammell, the universities minister, has suggested that the Church should pay the full tuition costs for theology students or that it should move students from classical three-year theology degrees into cheaper and less demanding two-year vocational courses.

The Higher Education Funding Council for England decided at a board meeting this week not to add theology to the list, pending a review of the importance of theology degrees.

The Church has two months to persuade the council to change its mind or to face the consequences.

These could include a downgrading in the quality of training of ordained priests or a £1.5 million increase in the Church’s training budget, which would be borne ultimately by parishioners.

Christopher Lowson, director of the Ministry Division of the Church of England, said that the withdrawal of university funding for students taking a second degree that was equivalent to or a lower qualification level than their first degree (known as ELQ degrees) would push up fees paid by students.

Those taking a second degree in theology pay tuition fees of £3,000 a year but these could rise to levels paid by overseas students of about £11,000 a year, he said.

As the Church pays the tuition fees for ordinands, it would have to meet the extra costs in full.

While the Church accepted that a less expensive two-year foundation degree might be acceptable for some ordinands, it would not be suitable for the brightest and best.

“Most people who become senior bishops or deans have studied theology at degree level. If you are going to lead the Church and negotiate with other faiths, you need a greater understanding of your own faith and how it has developed,” he said. Canon Martin Seeley, principal of Westcott House theological college, part of the Cambridge Theological Federation, gave warning that the move could lead to the closure of leading theological institutions.

“At a time when the social and public expectations of, and demands on, the clergy of any faith or tradition are increasing because of the social fabric, we need more than ever before to have people who are trained well,” he said.

Canon Judith Maltby, theologian, chaplain and Fellow of Corpus Christi College, Oxford, said: “It could be quite catastrophic for the Church.”

She said that the Church of England and its ecumenical partners, such as the Methodist Church, had been following a policy of ordaining a body of clergy that was as theologically literate as possible.

“We want clergy educated to degree level in theology, not just for service in the Church but to be better servants of their communities and in society,” she said.

“This [proposed change in funding] would make that prohibitively expensive and could also impact on theology as a subject in certain universities where ordinands form a significant minority of theology students.”

The Government says that it needs the £100 million savings from ELQ degrees to provide funding for students taking their first degrees. It adds that it has mitigated the blow of the cuts by increasing funding for part-time students from £20 million to £30 million.