The "xlerate with xl" initiative - run by the Prince's Trust and funded by the Hunter Foundation and the Scottish Executive - had been offered free to schools across Scotland, but many had turned it down, Sir Tom said.
An evaluation of the success of the programme is currently with Scottish ministers, but it is understood to show a high success rate in remotivating disengaged young people and guiding them back into education. The multi-agency initiative encourages pupils to make the most of their time at school, to become more motivated and to develop work skills.
Ewan Hunter, chief executive of the Hunter Foundation, said an internal evaluation by the Prince's Trust had shown that 90 per cent of 1,800 young people involved in xlerate with xl had gone back into education in a positive way.
"There has been a reluctance to engage," Mr Hunter said. "We don't know if this is just because it's new and the evaluation has not been seen yet."