Academics have already warned the government that its move to increase the number of teachers trained in schools will put long-established university teacher-training departments at risk of closure.
Now, subject associations have voiced their serious concerns over the plans, which will mean schools taking responsibility for training thousands of new recruits who previously would have studied PGCE courses.
Experts in English, maths, science, design and technology, the arts and RE have all expressed fears that the change will result in a loss of the teaching expertise that is needed to improve standards in schools.
Sue Pope, chair of the general council of the Association of Teachers of Mathematics, said she was concerned that the reform would lead to cuts in training opportunities for existing teachers. "University departments don't just provide initial teacher education, they also conduct research and run continuing professional development for teachers," she said. "If teachers are trained in schools, there is less opportunity for one-to-one support and reflection."
Many teachers who took part in a survey conducted by the National Association for the Teaching of English (Nate) said they were concerned at the impact of School Direct, which will replace the Graduate Teacher Programme.
"We are concerned about teacher supply - will schools take part in School Direct one year and not the next? Once university courses close, they are simply not going to reopen," said Simon Gibbons, chairman of Nate. "You will lose a lot of expertise. The universities don't just train teachers, they do research and run master's courses for them.
"This is an ideological move by the government that is not based on evidence. There is a move to make teaching an apprenticeship profession and to de-professionalise it."
Around a quarter of all teacher-training places for 2013 have been allocated to School Direct. The government believes the change will help schools to recruit and train staff to higher standards.
But it also means the number of PGCE students that universities can take on has been reduced in many cases, with academics voicing fears that courses will no longer be viable.
Annette Smith, chief executive of the Association for Science Education, said the move to School Direct could have "unintended consequences", removing expertise from universities. "I can see the logic behind this arrangement but if we lose subject pedagogy and research you can't rebuild it," she said. "Science education research is already fragile because it's difficult to find people who want to go into this area. There will be consequences for educational research and peer learning."
Lesley Butterworth, general secretary of the National Society for Education in Art and Design, has met civil servants to express concerns about the move to school-based training. "The PGCE is an exemplary, ideal model and we worry about its future," she said.
Andy Mitchell, assistant chief executive of the Design and Technology Association, will write to the Department for Education and the Teaching Agency to express his concern about the changes.
"There is a risk of the subject stagnating and not being able to move forward in the way it has been able to in the past," he told TES. "Big breaks have been spearheaded by initiatives and research that have taken place in universities."
Ed Pawson, chairman of the National Association of Teachers of Religious Education, said RE was under "significant attack", not only because of the teacher-training decisions but also because it has not been included in the English Baccalaureate.
But a DfE spokeswoman insisted that School Direct was proving "overwhelmingly popular", showing that schools saw it as the best way to recruit talented staff.
"The majority of this training involves schools working in partnership with higher education institutions, which have access to rigorous academic research but can tailor the programme to a school's individual needs," she said.