While EMAs do not affect state benefit payments, training allowances, which begin at pound;40 a week, can reduce the level of income support, housing and child benefits.
Kieran Gordon, chief executive of a Merseyside Connexions partnership, said the EMAs were seriously affecting choices made by 16 to 18-year-olds.
"Some families are heavily benefit-dependent and this catches them in a trap. Some work-based learning affects money coming into the family whereas EMAs don't. It seems unfair that people are discouraged from vocational training which might be the best option for them."
He cited one case where a young person was persuaded by her father in front of her Connexions personal adviser to continue on a college course she did not like, as her choice of training would have cut their benefits.
Eventually she dropped out of college and left home.
The same adviser was urging a young person to consider an Entry to Employment (E2E) programme, but her mother discouraged her because of lost benefit.
Just last week, he added, a young person asked her personal adviser for an application form for college. "When the adviser asked if it was for work-based learning or full-time education, the girl replied that she wanted the 'pound;30-one' (the EMA) as her mum had said that the other would affect her benefits."
He highlighted the issue in recent evidence to the education select committee investigating the national skills strategy for 14 to 19-year-olds.
"What we need is a package for young people that doesn't impact against them making the right post-16 choice," he said.