Nigeria's Information Ministry said in a statement on Sunday that the students of the Government Science and Technical College in Dapchi, Yobe State, are so far unaccounted for.
The insurgents stormed their school on Monday evening.
The authorities initially denied that any student had been kidnapped.
Amsani Alilawan, a teacher at the school, which has 906 students in total, said there were soldiers in Dapchi until last month but they were redeployed.
The kidnapping has raised questions about the military's repeated claims that Boko Haram are on the verge of defeat, after nearly nine years of fighting.
It has also revived memories of the 2014 mass abduction of more than 200 schoolgirls from Chibok.
On Friday President Muhammadu Buhari apologised to the girls' families, calling the incident a national disaster.
Former military ruler Buhari was elected in 2015 on a promise to defeat Boko Haram, after the jihadists grew in strength under his predecessor, Goodluck Jonathan.