The study of 160 Association of Colleges (AoC) members revealed that 94 per cent believe cutting EMA will prevent young people from travelling to study, particularly in rural areas.
Chris Morecroft, president of the AoC, warned that students are set to suffer a double blow, because college and local authority subsidies for student transport are also being reduced.
"There is a danger of students getting caught in a pincer movement between cash-strapped colleges and local authorities, which have also seen severe budget cuts," he explained.
"Our members are concerned that local authority subsidies may be at risk and even where subsidies remain, fares still may be out of reach for the poorest students.
"The abolition of the EMA will simply compound this, leaving the most disadvantaged students struggling to get to college to gain the qualifications they need to prepare themselves for a fulfilling and productive life.
"This may be an unintended consequence of the funding cuts faced by our colleges, local government and our students, but it flies in the face of the coalition government’s avowed desire to improve social mobility."
Morecroft called on the government to reconsider abolishing EMA funding, particularly for those students in their second year of college.
He added that AoC is "pushing for clarification" from government as to whether colleges will be able to use the new enhanced Learner Support Fund to help disadvantaged students with travel costs.
Meanwhile, the shadow education secretary Andy Burnham is supporting a legal case to challenge the removal of EMA from young people currently half way through their course.
According to lawyers, such students may have a case against government since ministers’ pre-election comments could have given rise to a "legitimate expectation" that EMA payments would continue for the duration of their studies.
"Once again, the government has made a rushed decision based on extremely selective evidence and before any alternative is in place – and once again, young people will pay the price," Burnham said.
"I am calling on the government to rethink its decision to scrap EMA, which flies in the face of its claims to value social mobility."
Unison, the National Union of Students and the University and College Union are backing the legal challenge.