The first intake of 26 students to Aberdeen University's pioneering course in the Highlands last week told Peter Peacock, Education Minister, to end the discrimination against part-timers.
Mr Peacock has now asked officials to investigate.
Part-time training is being hailed as the way ahead by ministers, local authorities, universities and the General Teaching Council for Scotland but students continue to be penalised. The first set of part-timers on the Strathclyde University two-year primary course had their fees paid but the latest recruits are being compelled to pay pound;565 a year by instalment as the scheme is no longer a pilot.
The Scottish Higher Education Funding Council is being fingered for its strict regulations over part-time students but a spokeswoman said that universities had discretion over how much to charge.
Cathy Macaslan, dean of education at Aberdeen University, said: "It's an issue that really has to be looked at."
Students on the part-time distance learning course at Aberdeen have also been told they will not be able to apply for loans from the student awards agency.