A national deal to fund the 12-week personal development courses ends this academic year, and local Learning and Skills Council offices say they cannot help.
Yorkshire and Humberside, East London, Lancashire and eastern England are particularly at risk, according to the trust.
The trust, the largest of the Prince of Wales's charities, was founded to help young people who struggle at school, who are in local authority care or who have been in trouble with the law.
Around 9,000 young people a year across the UK attend the courses to gain skills and confidence. As FE Focus went to press, 2,000 places were at risk.
The trust says 73 per cent of those who attend the courses, run by organisations from FE colleges to fire services, go on to employment or back into education.
A spokesman said they were still in talks with LSC offices nationwide to try to secure funding for the "flagship" courses.
He said: "Even if one of these vulnerable young people doesn't receive the support they need, that is a tragic waste."
But some course providers have already been told by their local funding bodies to give up hope.
Devon LSC said that it could not fund the pound;750,000 needed to continue the courses in the county because it did not have the money.
It also said youth unemployment was no longer a priority.
Linda Brown, managing director of Dartington Tech, a charitable training group in Devon, said time was running out. "There is so much press about getting young people out of their hooded tops and off the streets, yet one of the most successful programmes which manages to do this is facing a funding crisis," she added.
A spokeswoman at the LSC national office said: "Success in attracting learners has meant that all budgets are under pressure, and, as with all provision, it is always local and regional priorities that will shape the level at which it is purchased in the future."
DISABLED STUDENTS LOSE PLACES 3