More than 200 school and colleges have been damaged by the flash floods a few being washed away, said a government official.
Moreover, thousands of students in the flood-hit areas have lost their books, school uniforms and other educational items.
The disaster has struck at a time when the school examinations are hardly a few weeks away.
Many students in areas where the floods waters have receded have started rummaging through their damaged belonging hoping to find their books.
"I am looking for my text and note books. If I can find even a few things I will be lucky but I don't think I will be able to get any of my school essentials," Robina Shira, a Class 10 student.
There are many school and college students who do not know how to return to their educational institutions and prepare for the examinations.
However, Lirinda Sangma, another school student has not lost all hopes. "I have lost my books. But I am not losing hope. Instead, I have started reading and writing, whatever little I can," she says.
Lirinda's father Siljong Rechil Marak Sangma, whose house was damaged and standing crops destroyed in the floods, said, "I might not be able to send all my eight children to school. It is impossible now to raise money for fees, books and uniforms. However, if the government or the school authorities help, it would be a different story."
Chief Minister Mukul Sangma has instructed the district authorities in the flood-hit areas to work out the requirement for books and uniforms for flood-hit students.
"I have seen the quantum of damage...I have directed the district authorities to work out the requirement for books and uniforms...so that students are back to their schools," Mr Sangma said.