The closure reportedly affects 85 secondary schools, catering to some 120,000 students across the troubled state, a stronghold of the militant sect waging a five year insurgency in Nigeria.
The murderous group, whose name means “Western education is sinful” in the Hausa language, has vowed to stop children attending school.
“We reported to school on Friday last week (March 14) but to our shock the principal of the school told us he had received orders from the ministry of education to close down the school indefinitely,” teacher Suleiman Gana told AFP.
“He (the principal) told us the decision affects all public secondary schools in the state and was taken as a precautionary measure to safeguard lives of teachers and students from Boko Haram attacks,” Gana said.
A Borno state official confirmed the closure of the schools to AFP, speaking on condition of anonymity.
Deadly attacks blamed on Boko Haram have intensified since the turn of the year, with some 700 killed in more than 40 attacks in 2014 according to Human Rights Watch, making it one of the bloodiest years since the insurgency began in 2009.
In the restive northeast, tens of thousands have fled for their lives, either in fear of further attacks or after militants razed their homes and businesses.
A wave of attacks on education targets, including the slaughter of boarding school students in their beds while they slept, has prompted international condemnation.