The cost of paying substitute teachers has risen by 40% in the past eight years, according to the Audit Office.
In 2001 it cost £38m but last year the figure was £66m, the government-spending watchdog said.
One possible reason is an increase in maternity leave which means longer absences by new mothers have to be covered by schools.
In 2001, the Audit Office highlighted the amount schools were paying and said the bill should be reduced.
Eight years ago pupils could expect a temporary teacher 10% of their school days, that has now risen to more than 14%.
That is the equivalent of a pupil being taught for a year by a substitute teacher.
Auditor General Kieran Donnelly said despite telling schools to stop re-employing prematurely-retired teachers as substitutes, the number of days they teach has increased by 40%.
The cost of substitute cover has been tackled before by the government's watchdog, the Audit Office, but it seems previous warnings have not brought improvements.
The Audit Report said it was disappointed that the records kept by the Department of Education were not "rigorous" enough to help them manage the rising costs.