Training-providers have written to further education minister Malcolm Wicks to express their concern at the decision which they believe will mean students opt for secondary teacher training at the expense of dedicated FE courses.
They raise the prospect of FE post-graduate certificate of education students struggling to get by while training alongside secondary PGCE students earning pound;150 a week.
At the Institute of Education in London, for example, 100 students are training to become FE lecturers while 1,000 are on secondary PGCE courses - with both likely to end up teaching the same A-levels and GNVQs.
John Homewood, chair of the post-16 ommittee of the Universities Council for the Education of Teachers, told Mr Wicks: "Good new teachers are a scarce resource in post-compulsory education too."
Performance pay in schools - which will see experienced teachers get a pound;2,000 pay rise for meeting certain threshold standards - is already likely to attract lecturers away from the poorly-paid FE sector, UCET argues.
"The proposals offer a powerful disincentive to new graduates thinking of training for FE," Mr Homewood writes. "Applicants for post-16 work may now choose to take a schools teacher-training route with all the consequences that this entails, including the possible loss to colleges of many new teachers. Incentives need to be offered evenly if we are to avoid a knock-on crisis of recruitment to post-16 teacher education."