A study by JM Consulting for the Department for Education and Skills found that trainee teachers attract about pound;1,000 per year less than it costs the universities.
Costs at 12 of the 15 higher education institutions were found to be much higher than funding.
Universities have long complained that they do not get enough money to train teachers.
Two years ago, ministers were forced to give pound;3m to London university's institute of education after it threatened to drop its training courses.
Teacher recruitment expert Professor John Howson said the pound;50m shortfall could even be an underestimate and the figure could be more like pound;100m as schools are not paid enough for the work they do with trainees.
Professor Howson said the findings are embarrassing for a government that has promised to get tough with training providers, .
"If you want a high-qualify teaching force you have to pay for the training. This gap must impact on quality," he added.
The study looked at four-year BEd and one-year PGCE courses. It found that the average annual cost is pound;5,973 per student, but average funding is just pound;4,921 - a gap of 20 per cent. Design and technology is the most expensive subject, but institutions and courses that have find it hard to recruit students are most likely to suffer high costs.
A DfES spokeswoman said: "Ministers welcome this research and will consider the findings in the coming months."
Review of the unit of resource for intitial teacher training: study of provider costs is available at www.dfes.gov.ukresearch