The Educational Institute for Scotland (EIS) teaching union said previous financial support for Curriculum for Excellence (CfE) had not been spent in schools as intended.
The warning came after Michael Russell, the Education Secretary, announced an extra £1.4 million to help pay for text books and classroom materials.
Larry Flanagan, general secretary of the EIS, welcomed the move, but urged Mr Russell to ensure the money got to where it was intended.
"Quite a bit of the money that was invested before did not find its way down to school level and we have to make sure this new money does not sit somewhere in local authority budgets not achieving the purpose it was intended for," Mr Flanagan said after a speech by Mr Russell at the Scottish Learning Festival in Glasgow.
Mr Russell said: "This money is for secondaries and if you don't see this money then tell me because this money has to come to schools. It is meant for schools and I will do my utmost to make sure it gets to schools." Mr Russell used his speech to highlight new leadership courses for classroom teachers.
The Scottish College for Educational Leadership has been set up to encourage schools staff to develop their leadership skills even if they don't want to pursue a promoted post in schools.
The move follows research highlighting the importance of all school staff taking a lead in the running of their school.