The means-tested scheme was set up several years ago, to help impoverished trainee secondary teachers who might otherwise drop out of their courses.
But the introduction this academic year of pound;6,000 training salaries for one-year postgraduate students has resulted in the scheme's funding being slashed from pound;9 million to a projected pound;3.8m this year.
It means all training institutions have less money to distribute to needy students. Particularly affected are students on the first year of two-year postgraduate courses, who do not get training salaries until their second year.
The two-year courses cater specifically for students training in shortage subjects like maths, science and technology, who have some grounding in the field but need more time to boost their subject knowledge - for example, economics graduates converting to maths teaching.
There are only 386 students on such courses across the country, but they are a key source of scarce teachers. Two of the biggest training providers have already protested to the Teacher Training Agency.
Dave Miller, Keele University's programme leader for initial teacher training, welcomes the introduction of training salaries, but has written to TTA boss Ralph Tabberer asking for them to be extended to first-year students on two year courses.
He said: "On two-year courses, he scheme is the major source of support for people. Their needs are going to be greater than many of the other students, but the cuts are disadvantaging everyone on our courses.
"The two-year courses are seen as a very good recruitment vehicle. Most of these people, who have already done a degree, are making considerable sacrifices to help fulfil the requirements and become a teacher in a shortage subject."
Ray Bird, a married, mature student with a mortgage, on a one-year postgraduate course at Keele, said students like him had missed out on the scheme's top ups because institutions were directing what money they had at first year students on two-year courses.
He estimates his one year of training will leave him pound;12,000 in debt, including pound;4,000 of student loans, set against his pound;6,000 training bursary and a starting salary as a newly- qualified teacher of around pound;16,500.
Graham Frank-Keyes, secondary teacher-training admissions tutor at Manchester Metropolitan university, has raised his institution's concerns with the TTA.
Students on two-year part-time postgraduate courses or flexible routes are eligible for the training bursary, and he believes there is no reason for distinguishing between these different types of student.
"It does seem very anomalous and it does cause a lot of hardship," he said.
A spokesman for the TTA confirmed that the scheme has suffered as a result of the introduction of training salaries.