The Vanuatu ministry of education says it did not receive all the government funding promised last year and places affected by Cyclone Pam and the El Nino.
All government schools started their programmes this week.
But in Shefa and Tafea provinces many schools still have damaged facilities due to the cyclone while some parents affected by drought have struggled to pay fees.
The ministry in a media release says it only got 40 percent of the money promised by the government for the affected areas, and that has been paid out to schools and parents.
The ministry is calling on parents from the affected areas to make partial payments so students can return to secondary schools this week.
It says if the government provides the outstanding funding later year it will be passed on the schools and the parents.