Unicef, the UN children's agency, said at least 57 percent of schools in Borno state were closed as the new academic year began this month, with teacher numbers as well as buildings badly hit by the violence.
More than 2,295 teachers have been killed and 19,000 displaced, while nearly 1,400 schools have been destroyed in eight years of fighting, it added in a statement.
Schools were shut because they were too badly damaged or were located in areas still deemed unsafe despite a sustained military fight-back against the Islamist militants since 2015.
The agency's deputy executive director Justin Forsyth said on a visit to the northeast that the effect of the insurgency on education was "no accident".
"This was a deliberate strategy (by Boko Haram) to destroy opportunity for children to go to school," he told AFP in a telephone interview from the Borno state capital, Maiduguri.
Boko Haram's name roughly translates from the Hausa language spoken widely across northern Nigerian to "Western education is sin".
Its fighters have repeatedly targeted schools teaching a secular curriculum.
Boko Haram's kidnapping of more than 200 girls from their school in the Borno town of Chibok in April 2014 brought global attention to the conflict.
Forsyth said some three million children needed emergency education support but there was a huge shortfall to fund Unicef's programmes in the region, he added.
Some 750,000 children have been enrolled in school this year in Borno and neighbouring Yobe and Adamawa, which have also been badly hit by the fighting.
Overall, at least 20,000 people have been killed in the fighting and more than 2.6 million made homeless.
Nigeria's military and government claim the Islamic State group affiliate is a spent force but attacks, including suicide bombings, remain a constant threat.
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